If you look at the regulations, they are not charging fees for physicians, physician groups, non-physician practitioners and groups. It looks like it's just for facilities, and DMEPOS providers.
From the CMS Website, change request 7350:
Application Fees
With the exception of physicians, non-physician practitioners, physician group practices and non-physician group practices, providers and suppliers that are (1) initially enrolling in Medicare, (2) adding a practice location, or (3) revalidating their enrollment information, must submit with their application:
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An application fee in an amount prescribed by CMS, and/or
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A request for a hardship exception to the application fee.