I mean, I'd already spoiled some of the game for myself before playing. I knew I was going to kill Ryan, and the whole "Would you kindly?" thing. And even before I realized Atlas had been saying it the whole game, and hell, even after, I did sort of suspect that Atlas wasn't being totally straight with me. That in some way, I was being used. But I figured, "Well, he's doing it to defeat Ryan, who's the real evil here. And after all, his family did get killed. And since I'm the spawn of Ryan, he sees me as the optimal tool of his vengence." It sort of seemed justified to me, even if it didn't completely sit right with me the way the main character's entire life had been manipulated for that purpose.
But Atlas was the only confident I had in that madhouse, the only voice of reason. I didn't feel quite so alone and vulnerable as long as I knew he was on the other end of that radio (well, okay, I had firearms and plasmid powers, but whatever, you get the idea). And BOOM, suddenly that was taken away from me. Atlas wasn't just using me, he didn't even exist. And the person he actually ended up being was an even worse kind of monster than Ryan was. And what I had seen as justified now was an unforgiven offense.
I was reeling from the scene where Fontaine finally reveals himself; it actually hurt to have my trust squashed like that. And while I did gain Tennebaum as an ally (I took the good route), I didn't dare allow myself to trust her like I had Atlas, lest she turn around and screw me over too. I felt the kind of isolation I usually only get from Silent Hill games, because for the first time, I truly felt alone. And I hated Fontaine for that. I damn well looked forward to the opportunity to take my wrench and smash his smug, bald head in.