I don't miss them a bit and I haven't had any damage as a result of them not being there. The problem with the flaps is having to back up after pinching them in the rocks. It'll rip them right out and damage the fender liner. Best bet is just to keep them off unless lawdog says you gotta have them on.
I sold my mud flaps a week after I got my Tacoma. I knew down here they would end up getting ripped off in the woods somewhere. You should keep a eye out over on tacomaworld.com for sale section, I've also seen some single ones on ebay for sale. I would try and find something a bit more flexible to replace them with.