Either online, or just stash the checks away (do they expire?) and drop them on a new set of tires or something else useful when you make a once or twice a year trip to the bike shop that's an hour away.

As far as the actual program, it's probably an issue of paperwork and the hassle of dealing with the bureaucracy of getting their money when they need that stuff to pay bills now. Usually local bike shops don't have time to let monopoly money float around until they finally get that real check from whoever issues it. I could be extremely wrong, but that's just one guess.