Dilute phosphoric or oxalic acid will normally clean these off nicely. If you can't get cheap stuff from a chemist (do a search, UK suppliers have been listed many times on this board) then your chandler will supply a proprietory brand such as Starbrite for this purpose. Its also good for cleaning teak.
It usually occurs either:
(i) in streaks, coming from under steel fittings or where a mooring chain lies. If the fitting is stainless, this may indicate crevice corrosion in the fitting.
(ii) in little specks over the deck, caused by dust with iron filings blowing onto your boat. Always a risk if there is a nearby boatyard. Unfortunately if the filings are hot, e.g. from grinding, they tend to embed themselves in GRP and then are much harder to remove.
I got some rust stains on the deck last weekend from a polythene bag that had had a gas cylinder stored in it. I struggled with all manner of things to get it off. Finally took the plunge and invested 8 quid(!) in a bottle of Starbrite Rust Stain Remover. One squirt and it was gone! Highly recommended - even at 8 quid.