My short opinion: I prefer to use a clear (or UV) filter for protection on all lenses at all times, removing it temporarily only if I observe artifacts.
The chance of something flying at my lens during normal use is not actually a big concern in the environments I shoot. More of a concern is that if I accidentally ram the front lens element into an object (e.g. when getting too close in or shooting through a window or wire mesh), or if I drop it a short distance, the lens has a better chance of surviving, which allows me to shoot more adventurously and get better shots. It may also be accidentally scratched during regular cleaning, if you forget to brush it - a filter allows the lens element to be cleaned much less often. If you stick with high-quality filters (e.g. B+W MRC) you get very high transmission and not much glare in most situations.
In the end what it comes down to is because my budget for replacement parts is very limited, I'm willing to give away a little image quality for a little insurance. However, they are not at all necessary - front lens elements are specifically designed to be exposed to the elements and cleaned regularly, and some include additional coatings for this purpose (e.g. flouridefluorite coatings on Canon lenses). If you can get an affordable insurance policy on your equipment, that might be a perfectly acceptable alternative of similar cost.
