This is irrelevant if you're self-hosting your site.
WordPress.com is a free hosting site run by the company Automattic. Since it's run by a private company, they set the rules and restrict advertising.
WordPress.org is the homepage of the open source project called WordPress. You can download WordPress from this site and install it on your own server. Since it's open source, you can do whatever you want with it, so long as you follow the rules of the GPL.
Automattic uses the WordPress platform (freely available at WordPress.org) to run all of the sites hosted on WordPress.com. The names can get a bit confusing, but just remember
.com typically refers to a company and
.org typically refers to a (non-profit) organization. That should help you navigate some of the ambiguity.