Well...the standard method here (I think) is to use a rotary with the CarPro glass pads and CarPro Ceriglass. There are members who have used DA polishers, not sure if that's with the glass pads or regular pads, and gotten good results, so the Flex should be fine too.
"Real" glass polishing is done with machines that feed water through the center of the backing plate to flush and cool the surface, in our world we have to spray a lot of water from a spray bottle--either way it makes a huge mess.
There IS a method using special 3M sanding discs...they have about 4 different grades, that I'd like to try sometime. That would be with a DA and the coarser grades will haze the glass and then you have to refine it back to transparency--pretty scary sounding.
So basically your answer is sure, use your Flex, get the Carpro pads and Ceriglass, use lots of water and make sure the glass (especially windshields since they are laminated) isn't getting too hot.