Im not trying to brag or anything but im fairly stronger then the average person, I can run really fast and throw very far. Ive always been quite athletic, but ever since I got into sports ive had terrible endurance. I cant run very far at all withought completely gassing out.

Because you've never trained endurance seriously. Very few people have natural endurance and though you may run occasionally, you need to develop your endurance. Think of it as the same concept as lifting weights. No bodybuilding started out lifting 400 lbs on a bench press. They probably started out at 100 and added 10 lbs when their muscles could handle it. You must do the same thing for endurance. Start running 15 minutes and add a minute when your lungs can handle it. Within a month, you should be able to run a lot longer. Maybe even for an hour if you're in as good of shape as you think you are. Pylometrics, etc will help build power into your endurance after you have built up some basic cardio.

Zildijan is exactly right. Here are the specifics....

You have two different types of muscle fiber in your body. Most folks have a pretty even ratio. Fast-twitch, and slow-twitch. The fast twitch muscles rely in chemical reactions in the muscle cells themselves... ATP and creatine. They provide energy for short-hard efforts. Sprinting, throwing, lifting. They respond very well to resistance exercise.

Slow-twitch muscle fibers are thin and hairlike, heavily intermingled with blood vessels. They use oxygen to metabolize blood sugar. These fibers are the ones used for endurance, for "aerobic" exercise... Running, cycling, swimming, etc.

Most folks have a pretty even distribution... but some have more of one than the other. Those with lots of fast-twitch, as I suspect you have, excel at sprinting or weight-lifting or throwing...

Those with lots of slow-twitch make great distance runners, cyclists, cross-country skiers... That sort of thing.

You can bring your endurance up to the best level possible for you by doing aerobic exercise... By working at the proper training heart rate for longer periods.

Strength and endurance are just different things. I'm an endurance athlete, but don't have much upper body strength. If I wanted that, I'd have to work on it specifically. Likewise, you are strong, but if you want endurance too you'll have to work on it.

In short thats just how it works, when you are really strong you have less endurance, when you have really high endurance you have low strength.

Your body just cannot be master at everything.