Usually it's just a bit of surface rust, happens to mine to. The way I get rid of it is buy some muck off chain cleaner in halfords for £6 then literally get an old rag, a bucket of cold water, a sheet of cardboard (stops overspray getting on wheel and tyre) and a toothbrush and thoroughly clean it making sure all of the rollers spin freely and as much of the muck is off as possible on the chain, sprockets, front sprocket cover and chain guard. I then before lubing put a small amount of ACF 50 on a rag and wipe it carefully over the side plates of the chain and on the rear sprocket. I then put on the chain lube. Will need re-lubing every 50 miles in awful weather and I usually do it every 100 dry miles.
I clean the chain like this in winter about every 300 miles and in summer every 5-600. I reset the 2nd trip meter after it's done, so far chain is all good and looks pretty much new after 4-5000 miles. It's a ball ache and can take between 1 and 2 hours to do properly but has to be done unless you have a scottoiler, something I will be buying when I next get a chain.