I think the mud flaps offer a great bit of protection as compared to nothing at all, but rocks and such will get by them to some degree. Running boards offer much better protection and if you combine the running boards with the mud flaps your in excellent shape. I know that many people don't care for the running boards, so if your one of those that don't like, at least install the mud flaps for "Some" protection.

Like teknobunie, I have the running boards and mud flaps only in the rear. But I also have lake pipes to further aid in warding off rocks and such.