Car: Rust and paint chips

[Huckster]

I'm looking for some advice. I have a 2009 Toyota Matrix and it's showing a few minor spots of rust where the paint is peeling. The body shops only offer to paint a whole panel, etc. at tremendous cost.
Do you know of a reliable way of fixing these spots so that the rust won't bite further and deeper?
I know that these little paint sticks that the dealers throw in when they sell new cars are pretty useless.
I'd like to keep the car another 4-5 years.
Thanks

[auxym]

If you want it to look good as new, repainting the panel is unfortunately the only choice, though you could diy.

If you don't need it to look all that good, you can sand it down locally, remove all the rust, do a putty job if needed, prime with rust converter, and repaint with a can of spray paint which you can have made to match your car at an auto parts shop.

Or you could also let it rust. It's just esthetics. I bought a 2004 hyundai accent in 2009 for 4k, put 100k km on it in 6 years, let it rust until it had holes in the fenders, and still resold it for 1500. I did drop a decent amount of money into mechanic work though (normal stuff, brakes, timing belt).

[Spork]

On cars I was not particular about (not sure if that applies here) ... I sanded the rust off and just sprayed a little rusty metal primer on the metal.

[Papa Mustache]

See what one of those technical colleges (vocational schools) would charge you to use your car as a teaching aid. You buy the materials and they supply the labor.

[DangleStash]

Depending on the amount of rust, if it's just little chips starting to rust I highly recommend the little paint pens that are color matched to the vehicle.  Mine tends to get a TON of chips, so every oil change or so I just do a little walk around and touch up anything that needs it.  It's not the prettiest fix, but is only noticeable when the car is spotless and is much better than seeing the rust.

[HipGnosis]

The answer really depends if the rust is there because the paint peeled (like after a chip) or if the paint is peeling because of rust under it.
IF it is rusting from peeled paint, you can sand (or grind) the loose paint off and put Rustoleum Rust Reformer (or similar products) on the metal. 
If the paint is peeling because of the rust is under it, the only proven fix is to remove the panel and either treat the whole thing (both sides) or replace it (usually cheaper).