How do I avoid a rough surface after applying polyurethane
It is not unusual to have a "rough" coat as perceived by the user, happens to all. You should make sure to fine sand your base before you urethane, make sure you use a tack rag to clear the surface of bits that will can tribute to this. A tack rag is like a piece of gauze with sticky wax on it. You can thin the urethane with mineral spirits, a favorite mixture of many wood workers. Apply 1 smooth stroke with the brush, do not go over the same area again, you will just disturb and rough up the urethane on first stroke. Remember this is a multi layer process, multi step process.

Fine finisher sand in between coats, especially the first, that's were most the bumps come in due to surface dust, use 200-400 grit at first lightly and then go up to 600-800. Actual grits could get higher depending on your roughness. 

Summary. Sand surface well to high grit, clean with tack rag. Apply thin or normal coat. Sand, use tack rag again, apply, sand, tack rag, apply.