I am writing a dnd campaign based around doppelgangers infiltrating a country, and it will turn out that the character's main contact is, in fact, a doppelganger. The point of this is to make it really hard for them to trust any npc, but I'm worried this might make the campaign not fun for the players. Any thoughts on this?

It really depends on who your players are. My current group loves meeting NPCs, but my previous group would literally kill any NPC who joined their party. 

I think the plot is fine, but what's not fine is what you said about the point of it, "to make it really hard for them to trust any npc".

Don't try to control your PCs, don't try to make them think certain ways. They are the ones playing their characters.

Quote from WuDnD >>

I think the plot is fine, but what's not fine is what you said about the point of it, "to make it really hard for them to trust any npc".

Don't try to control your PCs, don't try to make them think certain ways. They are the ones playing their characters.

 This makes a lot of sense, I think I'm actually building things like this and making the campaign too railroad-like because I've only run a pre-written module that was a complete railroad. Thanks a lot for the advice!

So I think one way to do it is not through the plot, but through the atmosphere in your world building. You can basically make "don't trust anyone" a context of this world that is just baked into each character's background naturally... which may not fit your plot though, because you will lose the element of surprise...

a combinecd fairy tale world