... Tons of muck and brown crap, that did not get flushed out surprisingly...
Brake fluid is hygroscopic; it attracts moisture. That nasty muck most likely contains some water that has been emulsified with the brake fluid. Brake fluid does not cause rust. It's the... well, you know.
Rust in the area of the thin, rubber 'dust shields' can be a result of using a car wash power spray to clean the bike. Big, bad No-No as there are many spots on the Airheads that will permit high-pressure water to enter. Milky, water-polluted gearbox lube is just one similar concern. Save your quarters for the Vegas slots.
Flushing the entire brake system annually will go a long way towards preventing a repeat occurrence. The chore is much less time consuming with a handlebar-mounted MC that the dreadful under-tank MC's. Lucky me -I have both styles.