Brown algae is a curious algae (err, diatom). Typically, it appears in unbalanced or unstable tanks, such as newer tanks. When I started up my 10g tank with 6.5wpg, I was bombarded with it, for a little over a month, and I mean BAD. I kept scrubbing and cleaning. One of the keys to getting it to go away appears to be a very mature, adequate, and stable biological filter. On my 10g, I have a Fluval 104, and it was brand new. It takes roughly 2 weeks for bacteria to begin to establish, but much longer, around a month to begin maturing and become adequate; you might also notice this when cycling a tank. It really takes longer, given stable tank conditions such as fish load. After around 6 weeks or so, I cleaned the tank really good, did a water change, and it has never come back. I have no fish in this tank.
I also noticed that when I took my Eheim 2028 off my cichlid tank and left only 2 AC 500's, I got brown algae kind of bad. However, my pleco loves it, so I never have to clean the glass. He can knock out about half of the 100g tank in one night (tank is divided so fish don't kill each other, I just move him back and forth).
I'm from the planted tank camp, where we dump in all kinds of nutrients, use high light, and basically provide every condition possible that is favorable to algae. Plants are our weapon, but we must think about the foundation we provide for the aquarium in order for all things to thrive--a "natural system." First and foremost is the biological system because it does FAR more than just convert ammonia to nitrate. This means from gravel that facilitates good bacterial activity, to a good filtration system. Cannister filters are the filter of choice in this case, as they are meant to allow for a biological system. Power filters do not, and at a point cannot, and are meant for lighter loads.
If you clean your tank too much, too often, and think you're doing a favor by keeping things "hospital clean," you aren't. Cleaning should only be done for our aesthetics, like wiping the glass down or removing excess algae. Cleaning the filter or changing the pad is not aesthetic. Cleaning the gravel too often disrupts bacterial stability. Only clean it 2-3 times per year. I know what dirty gravel is...I've got monster cichlids that churn out more waste in one day than a beta will all year, and I only clean their gravel 3 times per year.
So give that a shot. I bet it will help.