Water + Iron = RUST, you will never stop it, usually it isn't so much rust as a rusty looking water, which will do no harm.
If you are worried about getting ALL the dregs of rust colouring and everything else out of there, run some WYNNS cooling system flush through there, but NOT for the 10 mins as stated on the bottle, use this in normal driving for 200 miles, this is what I do, then do a mega flush with hosepipe.
The flush will form as a congealed goo in the expansion tank, so this will need taking off to clean out thoroughly, dislodge the soft goo with a old stick etc, failing that boil it with boiling water.
This what I do and have been for well over 10 years.
tabetha