Is it a good idea to paint some surfaces such as the horizontal and vertical stabilizers, the elevator and rudder and the ailerons instead of using monokote to cover these surfaces? And if yes what type of paint would I use? A hobby store suggested I could use regular spray car paint and this would be fuel resistant.

I say go for monokote as much as possible. The airplane will look better, as the colors & texture of all the parts will match. Also, all the parts will be smooth & glossy. In my opinion, easier to clean, and repair is needed. Some paints tend to 'build up' and will leave an uneven surface. Not to mention the weight added, but I think this might be negligible..

Not to mention, trying to color match the paint & covering.

Surprisingly, monokote adds some tremendous structural integrity to the models. try it, cover and piece of balsa, then try to break it. Do the same with a painted part...

Save the paint for teh really hard to cover places, insides of engine compartments, plastic parts, wheel wells, etc...

As for fuel resistance, not all are. The hobby shop should be carring a line of 'fuel proof' paint; Centrury 21, and lustercote by Monokote (and are also matched to their lines of covering material) but they are not cheap. You can paint the part with regular 'Krylon' then give it a top coat of clear 'fuel proof' paint.

People have said that Tremclad (the anti rust paint) is fuel proof up to 15% nitro.