Build the Privateer wonder.

Otherwise it's difficult. Occasionally the UP holds a vote to appoint a guard for them, but the measure is short lived, maybe 2-3 years.

The only other options I see is to:

1. Carefully plan out trade routes away from hostile civilizations. This isn't always possible, though.
2. Lightly arm freighters & then build military starbases all along their route. Not very feasable, particularly since the bases themselves will come under attack.
3. Establish fleets to patrol trade routes and destroy enemies and pirates.

I've never armed freighters. I have put Sensors on them as "headlights" lighting up regions as they travel.

One tactic I do use is to have a reserve of them in the event of war, to immediately establish new trade routes. If you don't mind cheesy manuvers, you can buy freighters from other civilizations, immediately turn them around and establish a new route. I've found through testing that a route is established between their planet and your nearest one.

Late game, keeping Minor races around - even if they have no tech or other use for you - is a way to at least have some trade revenue when its just you and one other opponent.

if you want to protect freighters, build starbases! Why? because the AI will usually prefer to go for your starbases as a priority target. Starbases are then much easier to protect with ships. helpful hint - remember not to bother with starbase defences, those constructors used, will always be better off being warships instead.

Honesty, other than building the Privateer wonder, I just leave them be because I don't have the time to worry about them.

I play in a huge galaxy and my main focus is managing my planets so that I have a good balance between military, social, and research production. Frieghters in my games play an insignifcant role. For example, in my current game my weekly revenue (before expenses) works out to 83K BC, of which a measely 1,303 BC comes from trade. While I can establish up to 11 trade routes, I actually only have 4 active. The other races have sent frieghters to my planets though.

Other than managing my colonies, I spend a lot of time build ecomonic starbases to boost my military, social, and research production. That itself is very time consuming because I need to fortify them as well. There's nothing more wasteful then an undefended starbase during a war.

Anyway, frieghters definitely takes a backseat in my gameplay strategy and it is not worth the time and trouble to protect them from their point of origin to their destination. Leave 'em be. If you loose a trade route due to wars between other races, then there's nothing you can really do. Just set up another one that does not go into hostile territory.

Thanks for the feedback, I didn't think that trade could be so easily ignored, but now I know. Just one thing, what is the privateer wonder?

Try the Galactic Civilizations II Wiki. Its a bit dated (pre-DA), but chockablock with GalCiv2 goodness.

You got a Precursor Mine (700% manuf tile) after the 1.50X patch? I have never seen a 700% manuf or research on any planets since the patch.