To be fair, both Gilgamesh and Emiya-Archer aren't really what you'd think of when you say the word. I mean, both generally use weapons other than bows. Basically, every type of weapon aside from a bow. Archer generally either uses his swords or UBW, which is just a shit-load of swords. He does, sometimes, use his bow.....but to fire a Noble Phantasm in the shape of a lance. Gilgamesh doesn't use a bow at all, and he is Archer-class. He just straight up fires an endless amount of weapons of all varieties at his opponents.
Consider this, and the fact that Tohsaka had only seen Archer use his swords up to that point....her comment makes sense. It's less 'Hurp-a-durp. Archer class are archers,' and more 'Well shit. You do have the abilities of an archer. Despite only using swords up until now.'