Well... it actually
is, but I am pretty sure they have some sophisticated dust collection and environmental mitigation hardware on the machines that do it. Specifically, I'm thinking of PCB drill/router machines; which primarily work in FR4 fiberglass PCB material.
More on-topic to the actual question, though... I have seen on TV people who build boats (manufacturers, not just guys in their garage) use trim routers on fiberglass panels to, well, trim. Usually they are wearing a respirator; sometimes a full hazmat bunny-suit (and when they aren't, I just sigh and shake my head). Consequentially, I would tend to expect a CNC router to be able to do the same general thing... but you're going to have to do something about the hazmat situation that doing so will generate. Not only will it mess up your skin and lungs, the fiberglass dust is abrasive and will eat the linear slides and bearings of the router. I would also tend to expect your tool life (i.e, the router bit or endmill) to be comparatively poor, because of the abrasive qualities of the fiberglass. Some sort of coolant will be required; not only for the cutting tool itself, but to keep the resin in the fiberglass from melting (flood coolant would also help with the dust situation).
If possible, waterjet
would be better. I haven't checked recently, but waterjet machines used to be upwards of $100K... and I suspect the good ones still are... so prepare for a bit of sticker shock there. Waterjets also consume abrasive media, and have a variety of consumable components in them for "focusing" the jet. These can get expensive... but, on the other hand, when you add up all the expense with dust mitigation, and going thru cutting tools, the router may end up being comparable in running cost (there's too many variables here to make a generalized statement).
Unfortunately, I'm afraid I can't recommend a specific machine; because all my equipment is either DIY or a retrofit of some sort.
You mentioned 3D printing... is your experience primarily with off-the-shelf machines (like a Stratasys), or have you built your own RepRap based machine? If it's the latter, you may wish to consider a machine with a more "open" design - one with step & direction based motor drivers, a PC based control that uses standard software (Mach, UCCNC, or something like it), etc. For example, Haas has their own control system; and if there's any issue with it, you more-or-less have to go back to Haas for service. If you have the skills, an open machine can be fixed or upgraded yourself, with parts from a variety of sources.
In any case... good luck!