So, I'm of the bwana school of thought here - hoods give much better protection. When I got my first DSLR, I followed the sales dude's advice and got a regular Hoya UV filter along with the 24-105L. I can't say that I notice any difference in image quality at all, but I do get the sense that with the filter on, the lens is more prone to flaring, although in fairness, the few times that it's happend, I didn't have the hood on, and on one occasion the flaring actually made the image nicer

I did, however, stop using the UV because I felt the hood provides ample protection and when travelling I found it too much of a hassle to swap betwen CP and UV filters.
I buy hoods for all my lenses, and use them religiously, even indoors. With one exception - the 50mm f/1.8 II. That hood is too cumbersome and doesn't exactly provide a lot of protection.
Nevertheless, recently I found another problem. I've always had difficulty getting the lens cap on and off with the hood on, particularly with the 24-105L. To get around this, I bought a no-name center-pinch cap (you know, like every other brand makes), which makes this easy. But I find, when the camera is in the bag, with the hood on in reverse (otherwise it doesn't fit), the friction in the bag often causes the cap to come off, leaving the lens to the cap sliding up and down against it. I have the same problem with all my lenses except the 10-20mm (hood doesn't take up much space) and 50mm (fron element sits pretty deep). So I've started investing in good UV filters. Hoya HD models are pretty clear - you can barely see there's any glass in it unless you turn it to reflect light - and has some fingerprint resistent coating.
So far I haven't noticed any ill effect, and with the hoods on, flaring hasn't been an issue so far.