In space, there's no horizon! Your little ships are visible from beyond their own tactical range and get shot down before they do much good. They are too small to carry effective defenses. I'm sure the a small craft like a fighter would need hefty hardware to power a shield strong enough to protect against a full sized capitol ship's phasers or what-have-you. And to top it off, your sending real life people in these eggshells to get fried.
In my experience, one of the flaws when it comes to Trek-based fighter discussion is the assumption that fighters would be used against capitol craft, and I don't think that's likely except in rare occasions (as we saw in DS9, where they were part of a combined fleet). If we assume they're essentially extrapolations of real fighters, then they're primarily going to fight other fighters and small craft. This is how they behave in Star Wars and B5. They never engage a capital unit unless they have a whole lot of help, or unless they can employ a strategy that gives them an advantage (Rebels vs. Death Star, which was still likely suicide but logical since the DS was built to repel capital ships).
I think the other potential advantage human-piloted craft might offer, depending on the circumstances, is that they can use institution and even recklessness to win missions that a computer controlled drone might never succeed in. It would depend on a number of things.