Muggles were afraid of and far outnumbered wizards, and Hogwarts had untrained ones.
As your own quote says, Hogwarts was founded when a fear of magic was common.
They built this castle together, far from prying Muggle eyes, for it
was an age when magic was feared by common people, and witches and
wizards suffered much persecution." - Harry Potter and the Chamber of
Secrets, Chapter 9 (The Writing on the Wall)
The Founders had to hide Hogwarts because many Muggles feared magic. Muggles far outnumbered wizards, so if Muggles decided to destroy Hogwarts, they'd likely either succeed outright or else do a lot of damage, even if wizards are more skilled generally. Mobs and guerrilla tactics can eventually defeat even the most skilled opponents, especially if their numbers are small. We know there are far more Muggles than wizards, so the Muggles would either win or decimate the wizarding population in a Muggle/wizard war.
In addition, while the faculty might have a better chance of defending themselves, the majority of Hogwarts would be young wizards being taught to use magic, so they'd be relatively defenseless. Hogwarts would be an easy target for Muggles trying to lessen the number of wizards. If the Muggles knew of a place where they were training young wizards to do magic, of course it would be an obvious target. Not only is it somewhere that only wizards would gather, but most of them would be untrained students and therefore easier to kill.