I have a group of six that I am DM over and one of them is a aaracokra bard. They are all level three and flight speed seems a little overpowered. So how do I counteract this in fights and regular everyday encounters?

Most encounters that happen inside will negate the advantages of flight. Plus the dangers of falling are huge and are very real.

I’m running a campaign with an aarakocra PC and I’m ignoring his flight when I plan encounters. Yes, sometimes he has a huge advantage over the other PCs in an encounter due to his flight, but other times he’s stuck on the ground with the rest of them and he’s at a disadvantage there because the other PCs are using all of their racial abilities and he’s not able to use all of his. It all balances out in the end.

Things I've done... not because of balance, but just because I like being an ass to this certain player (it's all in fun):
Made it too windy to stay aloft - has to pass CON saves each round to stay in the air or start suffering exhaustion.
Low blanket of fog - within it things are lightly obscured from each other, from the outside you suffer the blind condition in relation to things within.
Creative goblins with (in??) catapults - take 2d6 goblin cannonball damage!
Flying kobold from out of nowhere with a net - yup, thought of it on the spot... made no sense for him to be there... but he was.

Anyhow, plenty of creative ways. Jut got to play to the table. I can pick on this player like I do because we are good friends and he knows in the end that I'll never let anything happen to him from DM shenanigans... except for that one time.... ok, make it twice.

Just move a lot of fights indoors, or use monsters with ranged attacks.  Send the manticore chasing after him while the melee guys are there unable to offer any help.

It requires creativity, but there's ways to do it.  If you can give as many enemies as you can some sort of ranged attack, do it.  If they fly too high in the forest, the branches block their view.  Give your casters spells like Earthbind, ensnaring strike, hold person, etc.  Again, it requires creativity, but it's not as difficult as other people have made it out to be.

Finding ways to mitigate or make it difficult to fly will be your friend here, such as above suggestions. Environmental conditions (wind, rain, storms, debris flying around, heavy low tree cover; inside environments), traps (magical such as electricity that zaps them and makes their wings seize up and sends them falling; nets, blankets thrown over them, etc), and plain logic (other enemies nearby will be alerted if they see it).

However, it shouldn't always be the case - there should definitely be times where the ability to fly does benefit them. Or else why bother playing that character? So letting them enjoy that aspect of their character is important, while still making it occasionally challenging to the point of even being a hindrance for them once in awhile. So for all the times you make it a little trickier than usual for them to fly, once in a blue moon throw them into an awesome encounter where some enemies are land-locked but some are flying (bandits who tamed a giant eagle, perhaps? Steep cliffs with angry flying snakes that are easy to kill but require someone to pick them off so the team can safely climb?) so the flyer can really feel that choosing that race had a positive impact.

Remember to let them shine sometimes since flying is fun. However, it is a huge risk and any battle with ranged weapons in it will put the flier at risk.

An encounter with a few melee and three longbow wielders could go very badly for the bard. Let's say the bard is flying at 40', the longbow opponents have 2 attacks each (pretty typical in tier 1), they prirotize shooting the bard because 1) they are flying and 2) they are a caster and 3) up in the air they have no cover. Bard hits zero hit points, plummets to the ground taking falling damage and an automatic death saving throw failure if not being instantly dead for taking max hit points in damage.

There will be enemies and encounters where flying is the same as immunity but it is very situational and everyone else in the party is still vulnerable so I wouldn't worry about the one character and throw in encounters against mixed ranged and melee attackers (or flying creatures) to keep the players on their toes.

I'll second what David42 said.  Flying can be a huge benefit in and out of combat for the player and party, so let them use it.  But Flappy Bard can become #1 target for ranged attackers and casters.  Tack on any fall damage and the player should learn pretty quickly to be careful.  You can turn it into a high risk, high reward option.

First off Aaracokra can only wear light armor or be unarmored to be able to fly. For him to be able to hit others ranged he would still be in range of enemies just make sure to have some archers or casters in fights. Also some encounters can be in dungeons with low ceilings to minimize him flying. Players make certain choices when they create characters because they have something specific they want to do. I think as a DM you should put them in fights that allow them to take advantage of the choices they made and put them in encounters where they are challenged and their usual gimmick doesn't work. Like an archer character allow them to be at ranged in some encounters and others have enemies set and ambush to mitigate their advantage with distance. You can do this sort of thing with any class really. This causes players to feel like heroes when they can shine in a certain fight and other times they are forced to work as a team. Example: The wizard may feel the need to dimension door the fighter or barbarian if they are needed to be within melee of someone.

https://www.dndbeyond.com/spells/earthbind

You dm for them the same way as any other character. Don’t sweat the small stuff. 

oh no he flew up one time over the tall walls and let down drawbridge   Let him. The challenge wasn’t in the drawbridge  -  it comes later  

oh no he flew up to the window three stories up bypassing my devilish climb checks. Let him. The challenge for him isn’t the climb it’s the  passive perception checks of the guards or the social encounter with the long hairs mass beyond the sill. 

On no he’s taken to the air and is shooting everyone thirty feet up out of melee range. Making a mockery of this important encounter, making the fighter feel stupid, the wizard impotent and the priest wishing he could ride his spiritual weapon. Let him and have many ranged bad guys shoot him out of the air. Oh look an obvious target looking menacing above all the limbs and legs locked into deadly melee. 

I second earthbind! Also, you can have encounters either have flying monsters go after him specifically, have dense forests with a good canopy for cover, or small buildings your attackers can take cover in. He'll stop flying if a Roc is headed his way wanting a snack.

Don't try to counteract the advantages of classes or races directly. Just design the encounters you would normally design. Sometimes they'll go normally, and sometimes he'll seem overpowered or extra safe. It's really no problem if you put the PCs up against a bunch of zombies and he just can't be attacked. If the PCs are losing the fight, the fact that he's up in the air won't change that.

There's a big difference between one player being able to fly, and the whole party being able to fly. Encounters rely on a team.

Typically in an encounter - unless deliberately designed to only have melee enemies, like in the zombie example - you'll want a mix of melee and ranged enemies. Spellcasters and bowmen can always ruin his day.