I think the Reed Johnson injury might be the one that hurts the Jays the most in the long run. I love BJ Ryan, but I don't think over the course of how long he's supposed to be out that it'll hurt the team more than 2 or 3 wins, if that, assuming the rest of the bullpen pitches about as well as they've pitched so far. And losing Glaus's power sucks, but in theory, Wells, Thomas, and Overbay should be able to pick up the slack there (even if they really haven't so far), and he's not supposed to be out for very long, anyway.
The hitters just aren't getting anything going, though. Johnson was hitting pretty well before he went down and Rios just doesn't seem to hit as well in the lead-off spot as opposed to lower in the order (he hadn't gotten on base since Saturday until he had a double in today's game). Thank God the starters have been great the last time through the rotation (save for Burnett's start against the Tigers), or they'd be in the middle of a huge, probably season ending-before-it-could-get-going losing streak.
EDIT: Well, Rios just hit a big home run to give the Jays the lead, so what do I know.