Ponies are just shorter horses. Same species, no problem there.
Short stallions can perfectly well cover tall mares if the mare is put in a bit of a hole or any other arrangement to help with the mechanics.
It is not however a very good IDEA, because rather than something evenly middlesized, what you tend to get when you cross animals of vastly different sizes/proportions is a foal with some momma-sized parts and some daddy-sized. Thus you can get a giant tank on wee short legs; or a pony with a huge clunky head and neck; or other weird and not really desirable arrangements. (Dont' argue about genetics, I am a biologist -- I am telling you what ACTUALLY HAPPENS the majority of the time when you breed two very dissimilar horses)
There is an additional reason not to put a small pony mare to a large stallion. While the foal will not grow *as* big as if it'd been in a larger mare, it still has a significantly higher chance of being large enough to cause problems being born. So you can end up with no foal at all, sometimes no mare either, and lots of bills.
Really, horses should be mated on the basis of "this is a superior mare, what stallion can I find that will maintain her good qualities an improve on her weaknesses". Period.
Pat