Dealing with Pirate / Raiding Trade Routes

How can I adequately deal with either pirate or nations who raid trade routes? It seems no matter how many fleets I create I always end up with an area that is susceptible to raiding.

I know with pirates I can just take over their occupied areas, but for other nations it seems to be a sticking point. One or two trade routes can wreck my economy, but having a large fleet to cover every inch does the same. That's even with upgrading all farms etc to max.

If we take the Barbary States for example, they will disrupt trade early in the game and I can only deal with them via launching a ships to fight, launching ships to invade and take them over, or making peace. All of these options disrupt early starting positions to trade in the trade routes.

Typically I play as the British / English if that helps.