I'm assuming you mean the individual pole pieces have rust on the top of them, as Stratocasters don't tend to have pickup covers (which can be easier to clean and polish)
First off, remember that removing rust isn't necessary to having the guitar sound good, and in fact that vintage aged look can be very desirable.
Second, most ways to clean them result in small metal shavings/flakes coming off, and you will never get these off your magnets, so your pickups may end up looking worse after cleaning.
But, if you do want to clean them, use some WD-40 or other penetrating oil on a rag or Q-tip and rub. This will get rid of the roughness. Then use a dry cloth to wipe up the excess. Dont get any on your paintwork though.
Personally I wouldn't bother, but if I got a guitar that had pickups that were so rusted they were flaking off everywhere - I'd just buy a new set of pickups :-)