Bondo will attach to most non oily surfaces, especially if they have been "roughed up" first with some sandpaper. But, if the rubbery surface can flex, the bondo will crack and break off. Bondo has a limited flexibility (very). Can't really tell from your pic on what the rubberized surface you speak of is.
There is vinyl trim paint that will paint fabric and won't crack off (like your shifter boot). Again, without understanding what surface you mean, hard to recommend a product.