You should use galvanized or stainless steel fasteners.

You won't be able to prevent those fasteners from rusting in wood as long as they are exposed to weather.

Buy some NAPA "Rust Treatment". Follow directions on bottle.Paint any exposed nails or screws with it.
It works great!!!
Mike

Rustoleum also makes a rust reformer. It really works. I've had no bleed through for at least 10 years.

try this stuff

http://www.por15.com/PRODUCTS/COMPLETEKITS/SUPERSTARTERKITS/tabid/102/Default.aspx

I would use all stainless steel, unless the added cost is so much higher to make it prohibitive, but it is all that labor - and hard work.
Galvanized may be sufficient..

Thanks for the tips. I'll be trying one of the products very soon. I didn't build the deck. It's an exisitng deck that I'm re-painting. I guess during the cleaning and scraping some nails are getting exposed. Not sure what they used to build it. Probably gavalized because some rust out and others don't unless they used a mix for some reason.

Anytime you have a rusting nail head it is usually not just on the surface but also underneath the top. No matter what you do to the surface of the nail the rust will continue underneath. The best way to deal with rust bleed from a nail head is remove the nail head. Go to nailheadgone.com, it only takes 10 seconds to remove a nail head.