Mostly I use both filters and hoods, especially on lenses I use all the time (35/1.4, 50/1.5). But with more specialist lenses, with which I'm seldom wandering about, I'll often use a lens cap instead of a filter (75/2, 90/2.2) but still with a hood.And with a very few lenses I either can't or don't use filters or hoods, so I use the cap a lot.
A really brilliant cap, that you can use with the hood on, is the OpTech "Hood Hat": see
http://www.rogerandfrances.com/subscription/review optech shower cap.html
Cheers,
R.