Using something like windex, or any other product containing detergents, is a bad idea. I think the coatings will be okay, but they leave a residue - which can only be removed by basically rinsing with other solvents (including water).
A really nice solvent for cleaning glass surfaces is isopropanol, or about 50% isopropanol in distilled water. It is safe to use on most coatings (though i can't guarantee anything), and any left behind will readily evaporate.
The difficulty is sparing the coatings, not cleaning glass itself: Glass is quite resilient to mechanical damage and nearly impossible to damage using solvents, but the coatings are much more sensitive.