I haven't heard of anyone doing this, but I guess it's possible but i don't think it would look very good. I think the paint would chip/crack from the flexing of the cover from being opened and closed.
I would recommend against it. The resale market for your T-cover, if in good shape, is very good and it can fetch a good price. So, instead of painting it, I would sell it and use the proceeds to pay for a fiberglass hard cover, painted to match.
I like that the factory cover is hinged in the middle, so that's why I really wouldn't be happy with the fiberglass one., although the fiberglass is much prettier. I thought painting it might be a great answer, but guess not.
I also like the factory cover because of the hinged middle. The fiberglass covers look really nice but they sit a little high and obstruct your view out the back window. The factory cover is a lot easier to remove when you need to haul things that protrude above the bed height.
The tonneau cover can be painted. Plastic is painted all the time. It just has to be prepped properly....How many people are told the plastic bumpers cannot be painted? (A lot)
What color were you thinking of painting it?
I think a dark color would look nice because of the black trim/rubber that would have to remain black.