This page lists all the possible causes of these symptoms:
http://www.medirabbit.com/EN/Respiratory/Differential/respira_diff.htm
This site has info on treating URIs
http://www.medirabbit.com/EN/Respiratory/Bacterial/URI.htm
We had a bunny with what seemed to be "snuffles." For a while, it was controlled with children's allergy medicine. Then it came back and was treated with antibiotics. Then it came back and was treated with antibiotics and anti-inflammatory meds. Then it came back and we had no idea what was going on. We had a lot of diagnostic tests done, to see if it was possibly a tooth issue (the bunny was a netherland dwarf). We had x-rays done to check the teeth. On those x-rays, the vet discovered a mass in the chest cavity, near the heart. We went for further diagnostics at a specialty vet and the vet school.
It was determined he had a large tumor of the thymus (a gland near the heart, involved mostly in immune system function). This type of cancer is not uncommon in rabbits. The location and his size made it inoperable, and the only other option was radiation. Because he was asymptomatic, we decided that treatment would only make his life more miserable, even if it would make it a bit longer.
Several months later, he had acute respiratory failure. He had been a bit less active in the week before, not eating as much, but still himself. In the morning he looked a little bad, breathing a bit heavily, so we got him a vet appointment. A few hours later he was gasping or falling asleep in between breaths, and eventually he was unable to breathe. The vet school did an extensive necropsy and confirmed the thymoma put pressure on the lungs and heart, and that caused his death. He was only 3 and a half.
It is dangerous to assume all runny noses are bacterial infections, especially if they don't respond to treatment. In our case, it did end up being something we couldn't treat, but if it were a tooth root issue things would have been very different. A lot of different and potentially deadly problems can cause "snuffles" symptoms.