I've been driving my car for the last 10 years with "brown" coolant. I've changed the cylinder head, water pump, radiator, most of the coolant lines, flushed the system, you name it. The coolant is still brown. I didn't do any of those things because of the brown coolant though. There are other products in antifreeze that can oxidize and cause a brown color to form. There is enough air in my overflow reservoir to cause this. It doesn't give me any less cooling capacity or pose any risk to my car. Bottom line: if you're concerned about rust, there are some simple tests you can do to check for dissolved iron oxides in your coolant.
Also, if you overflush the system, you can remove helpful scaling that forms due to the corrosion inhibitors in the antifreeze. This scaling is common in most heat exchangers and, while it inhibits heat transfer slightly, it keeps your parts around for a much longer time. So don't over-flush your system by doing it too often or with too much intensity.