The bus ride is on an "express" route meaning there are limited stops. Sometimes, it also means the bus can move "expressly" along the interstate. Sometimes, the bus is at a crawl in afternoon traffic.
As for a shorter bus ride: Ain't gonna happen. Most of the commute is the 33 mile part on the interstate and there are no stops there! There's no way to shorten that part. And the "in-town" part of the commute is short and on 35 mph roads. I doubt that is causing any problems.
One way to probably fix it: Let us bring the bikes on board the bus, like they do in Belgium and probably other countries. It would be an interesting test to see if the fenders kept breaking if they were shielded from the buffeting they get out on front of the bus on the interstate.