Several factors involved here to help bring you to your answer.
What type of conditions do you drive in? Bad idea to run low-filtration filters (K&N, CAI) in desert, dusty areas, etc. Clearly I see you're from Vermont so no desert, but if conditions in your area have a lot of airborne contaminants then it's a bad idea. Higher elevations, coastal areas, etc. tend to have cleaner air and thus reduced airborne contaminants.
To what benefit is a CAI serving you? Per se, if your jeep was a competition rig that you've invested countless $$$ in, a CAI would certainly benefit you better than it will as the ONLY power mod you've done to your daily driver.
I'm not trying to diss the aftermarket stuff b/c they're good products (well, some of them are
), just should be used in the right application. Best thing you can do to protect your engine is to keep running that dust cover (those catch a lot of the particles the filter normally wouldn't catch) and keep the filter oiled and clean. Be sure to keep the inside of your throttle body clean as well.