Even without directly opposing the State, the mere existence of alternative power structures poses an existential threat to it.

For just one small example, having fewer desperate people means there will be fewer volunteers for military service, making recruitment more expensive and sapping the budget available for foreign military aid.

Fewer military volunteers also means fewer people indoctrinated into the military mindset, further reducing support for military adventurism.

For another, organized people who work together to solve common problems are also more likely to recognize the shared humanity of those whom the State has declared to be enemies. It's hard to sell a genocide to the voters when they understand that they have much more in common with the victims than their own political leaders.