Alright, so to basically lay it out, you can do missions (some that can help people integrate into the game) that can get you cash, planets, and even a ship;) Basically, with the current NPCs of Federation and Alliance, you can do missions for either the Alliance or the Federation.
If you decide to work for the Alliance, and start attacking stuff the Federation wants, you will gain good reputation for Alliance and gain bad reputation, the only problem is the bounty system. Simply because if you attack the Feds, they'll probably put a bounty on you.
Anywho, there could be supreme benefits to getting high reputation. But, I'll let someone else think of that