I'm just using the numbers from the article. Here's the extract, relevant section highlighted:

The church enjoys tax-exempt status and claims more than 3.5 million members in the United States, but its secretive organization has remained controversial since its inception, and the Scientologists have repeatedly been sued by defectors or their family members.

Granted, membership claims may be exaggerated. But tax-exempt status is either true or false. And if true, then someone in U.S. government finds merit to their claim as a bona fide religious organization.