I'm not an expert, but here's my thoughts on the subject:
I wouldn't do this in the first place, because professionally made PCBs are so cheap now; and are drastically better than a milled one.
However, if you still really want to; there's a few hazards to watch out for:
1) Fiberglass dust is very abrasive. You need to keep it from getting in the machine parts. Otherwise you will kill your machine's accuracy very quickly.
2) Although not nearly as bad as asbestos, fiberglass still isn't good for you. My understanding of the hazard is that it's mostly similar to silica dust: it gets in your lungs, blocks the air from getting to the gas (oxygen/co2) exchange membranes in there effectively choking you; and because it's largely chemically bio-inert (it's glass, after all), it
never goes away. However, supposedly due to the shape of the fibers at a microscopic level (blunt ends, instead of very fine needle-like structures) it doesn't puncture cell walls like asbestos fibers do, and thus doesn't cause cancer (other things in the dust might, though).
3) If your spindle can't go fast enough, you will either get poor cut quality or a broken bit.
If I
had to do this; I'd probably run it under a dedicated flood coolant system; and make a "tank" of sorts to sit on the mill table that would keep the fiberglass dust contaminated coolant off of the machine parts. I'd also see if I could come up with some sort of rubber boots or plastic bag setup to help shield the machine ways. I'd wear a respirator as well (running it wet should take care of the issue, but you only are issued one set of lungs, ya know?).