Traveller publishing
Technically, no, you don't have to go through Mongoose to self-publish. There's a thriving 3rd-party group of publishers out there doing just what you're talking about. Gypsy Knight Games, Jon Brazer Enterprizes, Samardan Press, Spica Publishing, Terra-Sol Games, and my own DSL Ironworks are the ones that come to mind immediately, and I know there are more than that.
If you download the
Developers Pack, that will give you everything you need to get started publishing items using the Traveller rule set. If you're looking to publish things compatible with/set in the 3rd Imperium, it gets a bit trickier - everything has to be set in the Foreven Sector and requires the
Foreven Logo License. It seems complicated, but Mongoose has done a fair job of making it relatively painless.
If you have any questions about the process, I'd be happy to help. Shoot me a message here on COTI, or contact me through one of the links below.
EDIT: I should note, if you're going to self publish for money, you're pretty much guaranteed that it will have to be done using the Mongoose rules. License restrictions make it much more difficult to publish for other rule sets (CT, TNE, MT, GT, etc).