I use Jomax. Scrub it with regular water first and let it dry, then spray it with Jomax (found it at Lowe's). I can't remember how it says to mix it...I think it's a cup of bleach and 2 cups mix to a gallon of water. Their website swears its safe for all RV roofs including rubber. I've used it twice a year for two years now and haven't noticed any problems or areas of concern (and I really watch...kind of paranoid). It's supposed to inhibit mildew growth and, from what I can tell, it works pretty well. It's warm and humid here before my roof would turn nearly black in six months. Now it rarely gets slightly dingy in six months.
2012 Chevy Tahoe LTZ - HD tow package
2017 Rockwood 2703WS Emerald Edition