I made a project in a GitHub organization and made some commits there. Nobody else touched the repository. Since the default licence on GitHub is all rights reserved, do I maintain all rights to the project, even when it's in a organization?
GitHub user accounts, including organization accounts, have nothing to do with legal ownership of the copyright of work posted under those accounts. Your copyright attaches automatically to any creative work you make in a tangible form.
Code that you authored, posted under any account, is still under your copyright. Conversely, code that you post under your account that you didn't author (e.g., because it's under a free/open license that allows reproduction) is not under your copyright, but under the copyright of whoever authored it. The account of origin you choose to associate with code that you post to GitHub has no relationship to its legal status under copyright.
Note that if you are an employee, contractor, or student of some organization or employer, they may under some circumstances get the copyright of what you author (according to your contract and/or when you act as an agent of the institution). This doesn't have anything specifically to do with GitHub organizations, but if you posted code under a GitHub organization that represents an organization with whom you have a legal contract, having posted the code under the organization account surely gives the appearance of intending to assign copyright (as you sometimes do as a contracted agent) to that organization. Whether or not a court will agree that's what has happened depends on what your contract says and the contents of the repository. Again, this doesn't have to do with the GitHub organization account per se but how that account relates to some other legal corporate entity with whom you have a preexisting contract.
GitHub explains this in their Terms of Service:
You own content you create, but you allow us certain rights to it, so that we can display and share the content you post. You still have control over your content, and responsibility for it, and the rights you grant us are limited to those we need to provide the service. We have the right to remove content or close Accounts if we need to.
Note that giving someone rights ("licensing") is not the same as giving them ownership.