Here's a common way this happened.
1. You got an iTunes account first, before the predecessor of iCloud even existed. The Apple ID this created was associated with your regular email address.
2. You got a .Mac or MobileMe account early on. Those originally required you to use an email address at one of the Apple-owned domains (@mac.com or, I think, @mobileme.com, and maybe one or two more). Thus you ended up with another Apple ID associated with that email address.