You really think capital ships are going to be safer? During an epic space battle between two factions, anybody who sees a capital ship is going to be like "OMG! There's a capital ship! Deploy fighters! Take it down!". And if somebody sees those fighters, the capital ship crews will be like "Incoming fighters! Deploy more fighters!". It will mostly be fighters and capital ships dukeing it out, and nobody will care about freighters. Compared to capital ships, they're weak and can't deploy fighters, compared to fighters, they're very lightly armed and unmaneuverable. In a way, they're the "worst of both worlds", and most freighters only have civilian uses (hauling RMs or NPCs). But a select few freighters (those with speed and sensors) will prevail in combat.
This is because even though PLY-3000s, and YT-1210s are very useful, they aren't very much a combat threat, only having a single laser. If you're in a capital ship, and another capital ship, a squadron of fighters, and a PLY-3000 approach you, who are you going to take out first? I don't know, but I'm certain that it won't be the PLY-3000(assuming I'm not flying it lol). So if you want to stay out of combat, then a freighter is the thing for you. If you can afford it, an ATR-6 is even better than a PLY-3000 or YT-1210, being just as fast, with good sensors, but much better armed.