Have you done the bomb tutorial missions from Piri Reis in his shop at the Grand Bazaar? I was hardly using the bombs at all, then decided to do his missions and now I'm a convert.
Gonna murder some fools with tripwires, son!
Yeah, after doing his missions I pretty much started using bombs for everything.
Tripwires are kind of a pain in the ass to set up though, even after you have fully examined a group's patrol routes. Stupid citizens kept setting them off, so, to complete the tripwire bomb challenge, I threw caltrops everywhere and then sat right in the middle of the dancing guards to set up my tripwire bomb and make it explode.