It originated organically on Twitter as early users wrote “at” each other. Following that Twitter formally adopted it, and Mastodon imitated Twitter.

https://en.wikipedia.org/wiki/Mention_(blogging)#@_(at_sign)

Within Mastodon’s UI usernames are typically displayed as just e.g. @breaking, avoiding the visual noise of multiple at signs.

So it doesn't get mistaken for an email address.

It's on Mastodon though, the automatic linking wouldn't add mailto: at the front, think it's worth the cost of a few people not being able to post their email address without a mailto:

Referencing one of these username handles in external CMS systems (news sites, blogs, etc) might automatically convert them in Rich Text editors, or just Word processors, or even operating system toolings. Seems worth not re-using the same URI format.