This Act does not determine if Islam is a religion. It simply says that Islam does not qualify for tax exemption. This happens all the time.
They can still be a “religion” but we simply would not have to subsidize them with our tax dollars.
The qualification for a 501(c)(3) classification would also require not singling anyone out by name, but rather by “qualification” ... of which all organizations would have to be subject to the same qualifications.
Exemption Requirements - 501(c)(3) Organizations
http://www.irs.gov/Charities-&-Non-Profits/Charitable-Organizations/Exemption-Requirements-Section-501(c)(3)-Organizations
Publication 557 (10/2013), Tax-Exempt Status for Your Organization
http://www.irs.gov/publications/p557/ch03.html