Perhaps one of these threads will help you:

Oil Stain in Granite

Coffee Stain in Granite

Marble Poultice

Oh my :*(
you must be soooooooooooo upset.
I wonder why it was not sealed before they installed
it. Some places do a factory seal after they cut the
granite. Well too late for that and no sense thinking about
why. I would definitely contact your installer and see if
he/she can give you ideas on how to repair this.

Here are some links I found.

Natural Stone
http://www.natural-stone.com/stainremoval.html

Xomba Rust stains on granite
http://www.xomba.com/remove_rust_stains_granite_countertops

Here is a quote from the Housekeeping link below

".........Removing Rust

Rust is one of the most difficult stains to remove from marble, granite and other stone surfaces. Many of the rust removers available in stores can damage stone. We have found a great method for removing rust stains.

A product called Iron Out is available from most home centers and hardware stores. This product is a white powder that is designed for removing iron from water softeners, but also works great for removing iron and other metal stains from stone.

To remove iron stains mix I part Iron Out to 2 parts poultice powder (diatomaceous earth). Add water until you get a soupy consistency. Apply this mixture to the iron stain, cover with plastic and let it sit for 24 hours. After 24 hours remove the poultice and reapply if necessary.

For more information on iron and other stain removal see the book Stain Removal Guide for Stone, available from The National Training Center for Stone & Masonry Trades at 800-841-7199.

Here is a link that might be useful: Housekeeping Stain removal

Check out the "Stone Information" topic in the thread below.

Here is a link that might be useful: Thread: Miscellaneous Information [Part of the