I used to work there up until 2010 so I can give you the real low down.
1. They are definitely legit--they are a worldwide travel agency that's been around for over 30 years.
2. There aren't 48 stores anymore...almost all of them closed in 2008. There are now 17 across the US. You're in Boston, so you can use the one in Harvard Square--where I used to work!
3. There are often special web fares that aren't accessible to the stores. Don't ask me why--they were the bane of my existence. But if you see a mega-cheap fare online, just grab it. It won't be cheaper in the store or if you call. But do call the store to book your travel insurance, hotels, rail, all that other stuff. The personal service and expertise is better. Silvia, Zuzana and Megan at the store are truly excellent--they've been there for years and they know their stuff. For airfare though, booking online is usually best.
4. Anyone can use STA, they just have special fares for students, youth and teachers. But they sometimes have other, non-youth/education related deals.
5. Feel free to ask me any questions--I worked there for seven years.