Your method of transport shouldn't be causing BB failure but it still can't be good for the bike. Best case scenario I imagine it sliding and banging around back there. I used to have a truck with the common plastic bed-liner. It was like an ice rink. Without a bed-liner I'd imagine it being worse with metal-to-metal scraping. For the sake of your bike I'd come up with some kind of support system.

What type of BB is this? Square taper, Octalink, external bearing, press fit bearing? That might help us narrow down the cause.