Brown diatoms are usually associated with a new tank and will generally go away on their own. Other ways to help "encourage" it to go away are reducing the amount of light, making sure you're not overfeeding, etc. One of the primary causes is too many nutrients, particularly phosphates, in the water. If it's a real problem that just keeps going on, then you've probably got a phosphate issue.
In my case, the phosphates are added through the water changes from my tap--nothing I can do about that short of getting bottled water or an RO. Those options are too expensive for something I consider to be only a minor nuisance, so I've gone the filtration route. There are various types of media you can add to your filter to take out the phosphates. I use Phos-Zorb for one week about once a month, and that seems to work great.