UV will not harm your macro algae at all. As was said, it only kills what physically passes through the sterilizer. Normally you want about a 2x turnover rate through the UV... I've used one for years and still have a pretty good pod population.
It will not kill any hair algae in the tank... only spores which are in the water. They help keep algae from spreading and from disease outbreaks due to water borne bacteria in the tank.