How do I remove surface rust from a metal roof?
There at multiple products with which to remove rust from iron based metals. There are the mechanical methods which include sanding or wire brushing. Both of these methods can be done by hand or with a power tool.

The other method is to use a rust remover chemical. The common product is often referred to as "naval jelly". It is brushed on and then let sit for a while and then washed away. Often it is necessary to use a combination of approaches, the jelly and some concurrent work with steel wool or a wire brush. Make sure to use proper personal protection when working with the chemicals. 

Another very important part of removing rust is the need to properly prime and paint the surface soon after the rust removal. The rust removal process opens up the bare metal surface and it will re-rust quickly in the presence of any moisture.

In consideration that you would be working on a part of your roof be prepared ahead of time how you plan to deal with matching in the paint with the reset of the roof. It could get to necessary to repaint a larger area or whole side of the roof.