Banding together to collectively negotiate is fully compatible with the philosophy of capitalism. Under a free market, individuals are free to associate and disassociate as they please. What isn’t compatible is forcing other people to band together even if they don’t want to.

If you strike break, you will be arrested by the police.

If you compensate someone’s work with a wage, you will be arrested by the police.

You have no freedom to associate by your own will.