[CeeDub]

According to Jim Butcher's Dresden Files, the advantages muggles have are technology, coordination, and numbers.

No wizard or vampire will see a headshot from a sniper rifle coming. Then there are grenades, flame throwers, tanks, airplanes, drones, surveillance tech, and nukes. All of these can be used by any number of muggles, and their technology suffers none of the drawbacks that are common in magic. No FP cost, flat learning curve, usable by almost anyone, no time-consuming rituals. And there is no shortage of muggles. They coordinate. One phone call and policemen with guns arrive. One radio call, and dozens more arrive. Escalation to SWAT, FBI, National Guard, military? All possible.

Do not mess with muggles.

ETA: Muggles will rationalize a lot of weirdness and unexplained circumstances away - up to a point, beyond which they become relentless in their pursuit of knowledge/justice/power, with near unlimited manpower and resources.