Can you send ships to protect a trade convoy or protect freighters?

You can fleet your warships with freighters. As to protecting the little freighter ships that travel trade routes, I don't think fleeting works, and there isn't any commands that I know of that have your warships do convoy guard duty. Micro manageing your ships is my best suggestion.

Yea I know I can "fleet" to protect my freighters, but I am more concerned with the little tiny trade ships.

No dice there. The mini-freighters are the most vulnerable targets of war, even if it is not your war (as in it is your trade partner's war). Since they move after all the other ships, and even if you did know the exact route of every mini-freighter, you can't shadow them with your own ships except if you are at war directly with the raider. Then you can just destroy any ships that look like they are coming near the trade route by having ships in the general vicinity of the mini at all times. But if it is not your war, the minis are sitting ducks and there is nothing you can do about it unless you keep remaking the route, broker a peace between those two parties, or war on the transgressor yourself.