Though the advice above is all good, it sort of makes this sounds like an exceptional occurrence. It's not! Don't worry. Brown "algae" occurs in most new tanks unless certain nutrient balances are just right. Unfortunately, it is the sort of thing that can plague a tank for a long time, too.
Keep your water changes weekly, and your bioload (# of inches of fish in the tank) low, and scrub away once a week at the stuff. It should start to decrease over time.