The WD-40 trick works for the short term, but of course the rust will eventually return so you'll need to make it a regular part of your cleaning regimen. There are many other solutions, some more practical than others. You could clean the rust stains with solvent on a Q-Tip, then apply a coat of high temp paint to the recess in the head of the bolt. I actually did this on a previous bike using gloss black paint and thought the two-tone look was pretty neat. Probably not worth the time and effort however. Then there is the aftermarket solution known as chrome toppers (Hot Toppers is one brand). These are covers that plug into the recess in the head of the bolt, usually to make a regular bolt appear to be chrome. They seem to be very popular with the Harley crowd and can be found at many dealerships as well as in all the various catalogs like J&P, Drag, etc. The Ultimate fix is to replace the bolts with top quality stainless. This might make sense if you plan to tear the engine apart for other reasons anyway, but I seriously doubt I would ever consider it otherwise, unless I was building a show bike.
Jerry