As it happens, my local church is named after a saint who wasn't written up by name in the Bible. He was the founder of our church and his name was Emmanuel Peterson. (No prizes for correctly guessing whether the church uses his first or last name.)
I also found a non-denominational Protestant church called San Diego First Assembly. (That's probably cheating since the church was named after the city named after the saint.)
But as you noticed, naming churches after people (at least people not described in the Bible by name) is remarkably rare for Protestant denominations. The most likely reason is one you alluded to: Protestants have a different view of sainthood than the Orthodox or Catholic traditions. We have some reason not to put our trust in the names of people no matter who they were. As Luther said:
The more I read the books of the Fathers, the more I find myself offended; for they were but men, and, to speak the truth, with all their repute and authority, undervalued the books and writings of the sacred apostles of Christ.
Therefore, we Protestants are far more likely to name our churches after concepts, especially those found in the Bible. Alternatively, we use strictly descriptive names (cities mostly).