It partially depends on what you mean by 'rust spots'.
If you're just talking places where the paint has chipped or been scraped away and there is rust starting to develop, you're not in that bad of shape. Clean it well, get some sandpaper and sand down the rusted spot to bare metal (or as close to it as you can get). You'll want to sand around the edges of the paint around it as well to make sure that there isn't rust underneath that. The next step is something some will debate about, but I tend to advise getting what is called 'rust converter' and applying it to the area that had the rust- it chemically reacts with any remaining rust and effectively neutralizes it from spreading further. Note that it won't go through much thickness-wise, which is why you can't just put it on before sanding. Next you'll want to paint the area to seal it off from moisture so that it doesn't start to rust again. How exactly you go about this will depend on how pretty you care about making the car look. If you don't really care that much and want to do it as inexpensively as possible, get some Rustoleum spray paint (the kind that says something to the effect of 'paint over rust', they used to only make this but now make lots of other kinds of paint...) and spray over the area. They have a decent number of colors so you don't have to go with the classic primer grey. If you want to be fancier, you can get a primer paint to seal the raw metal area and then get something like the DupliColor paints to try and get close to the color of the car and then put some kind of clearcoat over it.
If you've got holes THROUGH the metal? Unless you're good at welding and metalwork, you're probably going to want to find somebody who can fix it for you. You can do something similar to above- grind out the rust and seal it back up- but you're still going to have holes that are going to let water (and salt) into places where it shouldn't be getting...
