I don't think it's a horrible idea, I was scared this was going to be something about them just in the bed of the truck, glad to hear that's not the case. They sell pick ups with back seats now, could you get one of those? Might cost a bit more, but it's a lot better then in the bed of a truck even with the cap on. If you really want them to have be in the bed, which would be a lot more room for them, I am sure there'd be a way to hook up some type of ventilation unit.

ETA: Yeah just thought about it..and saw Karen's post! If you kept the window to the cab open, I am sure it'd be fine, and you could probably get a cap with windows. In the winter, if you feel like it's extra cold, you could probably put Blankets back there.