Where possible I'd much rather keep an appropriate hood on the lens for physical protection. No adverse IQ effects at all.
Depends on the environment though. Sand, rain and spray, or when I'm shooting closeups of our pets (I've had my lens
licked more than once!
) would be good times to have a protective filter on there, just to keep the front element crud-free.
This is all a bit hypothetical in my case, as I'm still using a point-and-shoot with no hood
or filter, but I've got plans to upgrade and so have been thinking on this issue as part of my research. In short, I wouldn't buy an expensive filter to protect a cheap lens (that's just silly, I'd rather put the money toward a better lens!), I wouldn't put a cheap filter on
any lens full-time (IQ), and I wouldn't put
any filter on an expensive lens full-time (IQ).
It's worth noting that the lens on my current camera has survived nearly 5 years of unprotected use without so much as a scratch, despite such atrocities as being cleaned with the end of my t-shirt and the previously mentioned cat tongue action.
I'd be much more twitchy about mechanical damage to the internals that might happen in a drop or impact.