I think the biggest problem is client support, and that some people prefer using multiple devices for chat, including web based services (GMail, Facebook Chat etc).
Even with Jabber where you can have separate resources, it's not possible to have some clients use OTR and some not (with good reason, I guess), so you either have to add a separate, non-OTR account, or get used to turning OTR on and off manually. And I'm still looking for an iPhone Jabber app with OTR support.
I have a solution to this problem. For all of my IM'ing I use several IRC clients. I point them all at a single Bitlbee server which gates from IRC to various IM networks. I use the Bitlbee OTR plugin and assign each network its own OTR key. So no matter what IRC client I am using, I always have the same OTR key.
Even with Jabber where you can have separate resources, it's not possible to have some clients use OTR and some not (with good reason, I guess), so you either have to add a separate, non-OTR account, or get used to turning OTR on and off manually. And I'm still looking for an iPhone Jabber app with OTR support.