running is a cardio exercise, which will burn fat all over. the running itself will tone your legs mostly, but the weight loss will be more everywhere than one spot. i suggest keeping up with your running (which is a great start!) and doing some sort of ab exercise to target your stomach. i like six minute abs. you can buy the dvds or just do six minutes of different ab workouts, switching every 30 seconds. you can pick whichever exercises you want, targeting lower, upper or sides, which is why i like it. you can google different workouts if you want. a friend of mine downloaded the nike training app on her ipod and she LOVES it. she's been doing it for only a week and already you can see a sixpack starting. if you have an ipod or iphone, i would definitely look into that. another thing i like to do is while watching tv, just sit on the floor and do sit ups. i get so distracted by what i'm watching that i can do situps for a good 45 minutes without stopping sometimes and it's definitely a good workout. doing ab workouts on top of your running is definitely your best bet if you want to target your belly specifically, but at the rate you're running you should be fine :)
Running 3 miles is definitely a good start! I have been running for years and it is definitely a good way to get in shape or stay in shape. It helps you burn fat, and it tones your legs. It will also get you more active because bodies in motion stay in motion.
Here are a few other things that might also help you:
A few times a week you should try lifting weights. You don't have to lift a lot but it will help you tone your muscles. Just don't do it every day your muscles need time to rest. Lastly, maybe before or after every time you run you could add a few push-ups and sit-ups.