How can I toughen up my dog's paw pads?

Gradually build up how much he runs on the rougher surfaces. Dogs have to build up calluses on their pads in order to keep them from getting hurt. There are also dog booties for hiking you can try if you want to get started right away with running him next to your bike. It will just take time for him to get calluses, there is nothing to do except build them up over time, but the hiking booties might be of help to go longer distances even in the beginning.