Hi

 The bottom part of my frame has got scratched - possibly from being on a bike rack at the weekend or from being chained up outside work but i think it's actually from being in a bike shop this week

I'm thinking I should paint over it to stop it rusting but I don't know what kind of paint to use.  Any thoughts?

If wont rust.

 If it's Al al don't rust. If it's steel it takes time to rust, so unless you use your bike once every blue moon, you'll be fine.

Although scratch are part of the bike, and to be honnest if it's under the BB it's likely that it's the result of rocks sent flying from the front wheel.

 If it's really a pb for you, get some touch paint kit at halfords, or some nail varnish (this is not a joke)

Hope it helps

Juan