Are you sure it's rust or could it be rust colored stains and crud from oil and combustion? I've taken apart engines and found brownish or rust colored stains that were not a problem at all. The only thing that can rust would really be the crankshaft and a few other steel/iron parts that combatpigg mentioned. The other pieces are generally aluminum, bronze and other materials. Of course aluminum and other metals can also corrode in their own way.

Does the engine turn over smoothly and run well? If so, it may be no big deal.