ur dooin it wrong.
Naaah, just kidding, you'd be amazed how many people i've met who have trouble starting out in F3, a friend of mine actually wanted to thank the raider's after they 'saved' him, and was confused when they attacked him.
Anyway to me it seems like your playing Fallout like an FPS, and not an RPG (Although, this is just speculation, feel free to prove men wrong), the best suggestion i can give you without spoiling too much is to talk to everybody, esspecially the folks like Mr.Burke and Lucas Simms.
Also, if your really stuck, simply look up a good walkthrough on the vault.