The only downside I can see after having my phone jailbroken for a bit now, is that you can't use the newest firmware update from apple right away and still be jailbroken. Also, someone else can step in here, but it may not save all of your jailbroken apps/settings/preferences when you upgrade.
I couldn't imagine not having the phone jailbroken, though. I love that they call it jailbroken too, because, looking back, it really is liberating.
The phone functions exactly the same as before, only you have the ability to run 3rd 3rd party programs, ie jailbroken apps. From what I can tell there is no worry of permanently "bricking" your phone. The worst that can happen is that you must use itunes to restore.