As mentioned a couple of times above, comfortably riding a road bike takes technique and experience. Scan the road, identify obstacles, and if you can't avoid them you unweight and let your body flex rather than the bike. There's also a certain amount of HTFU.
A MTBer friend from out of town was visiting me and wanted to go for a short ride around my town. I loaned him a road bike. I was appalled at how much punishment he was taking. Every little bump was telegraphing up his spine and arms. I could see him wince. Less than ten miles into the ride he had enough neck and hand pain we aborted the rest of the ride and went home early. I realized too late he had no idea how to ride a road bike. And I know there are MTB techniques I've never mastered.