Hm, mostly it's just the ambiance that gets to me, as opposed to any particular fear or phobia in game. In real life I have acrophobia (vertigo) and deep water, but in games if I get the option I go cliff diving for the thrill of it. In skating games, I LOVE half pipes, bowls, etc places where I can catch absurd amounts of air because while I Do skate, these things terrify me, but in the game I can (at least vicariously), ignore my fears and DO these things.
I don't like schools or children in games though. I really don't like children in real life, and in games they're just plain creepy, and schools? They're FULL of children. If they don't CURRENTLY have children, they have the GHOSTS of the children. Hospitals are mildly creepy, but schools are worse.