You'll become neutral to a particular mini-faction of rebels if:

-you have no land bordering to them
-you don't have any ships in any waters adjacent to them
-(not entirely sure about this one) you don't have any agents in their province(s)

Essentially you must be totally cut off from them. Works with normal factions too.

If you're raiding these provinces and retreat to trade with them, it's vital that you leave the port intact. Sometimes it will be destroyed upon conquering it, you'll just have to rebuild it. Trade buildings don't need to be present in the provinces of your trading partners.