Well actually, weren't we all fooled in MGS 2? It's pretty hard to realise that the person who has been beside you and helped you for a long, long time, and even when you were betrayed by your organisation still helped you, would actually be a betrayer? Their plan wasn't exactly easy to see, and he still had some tricks left to pull...
Well, I don't know. Liquid has been talking with BB, he got information about many thing's Snake didn't have access to, so Liquid seemed much smarter in those scenes, however, probably only a few people in the world knew that info, Snake wasn't one of them...
Also, Snake had no idea what was going on. He was dragged from his house, put in a mission he didn't even want to take, and then felt like being betrayed by his superiors, Liquid had already planned this operation with the FOXHOUND group....
IMO...