I used to use a backpack. Then, I tried a messenger bag. The backpack made me sweaty, even on a short commute, and the messenger bag was always swinging around, hitting my arm, and catching on the seat when I dismounted at a stoplight or something.

I'm sticking with the latch-on Topeak bag, even though it isn't as comfortable for the train & bus part of my commute.

The possibility of a strap coming loose and catching in the spokes or the bag falling off is reduced to near zero with the rack bag, so it is a safety decision too. I realize this can be mitigated with proper bugeeing technique, but it just isn't worth the trouble to me.