I thought most filters like this functioned primarily for lens protection, and to complete the weather sealing of the lens?
Both are debatable.
The use of a UV/clear filter for lens protection is frequently hotly debated. As was pointed out, a filter can decrease IQ. With top quality filters, the IQ hit is so minimal that it's not noticeable in most
situations. But it will increase flare, no matter what - so when shooting a strongly backlit subject, you will lose a bit of contrast. Personally, I find filters much easier to clean than a front element (with the exception of the newest lenses with the fluorine coating).
As for weather sealing, Canon officially states the requirement only for a few lenses (16-35L II, 17-40L, and 50L). Chuck Westfall (Canon's technical guru) has recommended using a UV/clear filter on all sealed, non-supertele lenses.
Personally, I have B+W MRC UV filters on most of my lenses (not the 40mm pancake, and not the 600 II which doesn't take a front filter).