Well, if it's open source, it's likely that someone else has done an audit of the code, and even if I haven't looked at each line of code, someone else probably has (if it's popular enough). While it's possible to hide a loophole in popular compilers, I think this is hard to pull off. The government has a lot of resources, but it's also big, slow, and leaky, so I don't think it could pull off a sophisticated compiler loophole without people noticing.
On the other hand, an Windows operating system backdoor is a lot easier to pull off, since it's closed source and controlled by one company. The NSA could put hacks in Windows to capture message buffers from popular messengers, bypassing the whole encryption.