Bell provides a few clues about this later in season 2, when Olivia finally starts remembering their conversation. From season 2 episode 4 (Momentum Deferred):
Bell: And I'm afraid there's no avoiding what has to happen next. I pulled you out of a moving car. Momentum can be deferred, but it must always be paid back...in full. As I always said to Walter: physics is a bitch.
It would seem that momentum is conserved only within universes; you enter a universe with the same momentum you had when you were leaving it. Olivia was driving down the road at 40 or 50 miles per hour when Bell pulled her over, and when he dropped her back in her car was stationary (Obviously, since there was no one there to hold down the gas pedal, and also because it had just been in a crash). So she went flying through the windshield.
The problem I have with this explanation is that Bell did not pull her from her car; as you point out, she drove to the hotel unharmed, and Bell pulled her through in the elevator. This is a little hard to reconcile, but fortunately Bell provides another clue earlier in the same conversation:
Bell: How do you like your tea?
Olivia: I don't want any tea, I want answers.
[The frame stutters, and when it returns to normal Olivia has a cup of tea in her hand]
Bell: [Chuckling] You're still...a little disoriented from the time slips aren't you. Happened to me when I first came here. You're out of sync with this side.
Apparently crossing over the way Olivia did (And note that this time slip doesn't happen any other time anyone crosses over) screws with time slightly. A possible explanation is that Bell really did pull her out of her car just before the crash, but it took a while for Olivia to "catch up", so to speak. She kept living out an alternate version of her timeline for the next few hours, until the effect of being pulled to the other side finally caught up with her in the elevator.
Admittedly that's just speculation, and it's a bit dicey even by Fringe's standards for pseudo-science. However, it would help explain why Olivia is so disoriented when she wakes up in the season 2 premiere: she was expecting to wake up in an elevator, and instead she took a nosedive into the street. That'd mess with anybody's head.