This may be terrible advise but it worked so well for me that I'll share it. When we first got them running with the 4-wheeler I or hubby would go fairly slow in a straight line, if the dogs got too close on either side we would move towards them a little bit, not like a giant swerve but like a little turn of the handle and they would jump back out of the way. It didn't take long for them to learn tires= bad so stay away. Not that we ever ran over them or anything!!! I think it helped too that I have taken both of them on bike rides where they ran next to me, and I actually admit to running over both of them on more than one occasion on accident. That may have helped to teach them to stay out of the way!
When Chloe hurt her paws on vacation last year she got to ride on the 4-wheeler while Sydney ran and you could almost see Chloe gloating she loved it!!