My discs have chicken pox?

[hellforleather]

yeah they do but as mentioned before its the small particles of metal left on the disc from braking that rust that brown colour. if you scratch it with your nail it'll come off. the grade of cast iron that is usually used on brake discs just oxidises to produce a dull coating, dark grey ish.
if you really think its a problem do as the motorbikers do and use inferior but shiny stainless steel or take a leaf out of the motorsport book and go for MMC or a carbon-carbon composite

 

[Del Lardo]

Call that rust This is rust