Scientology is recognized as a charitable, pro-society ("bona fide") organization, not only in the United States of America but also in many other countries around the globe.
There is a great booklet about this here (www.thetruthaboutscientology.info), also available as PDF.
On the recognition as tax exempt in the US the booklet says:
Religious Recognition of the Church of Scientology in the United States of America
Following a two-year examination of unprecedented scope and depth, encompassing all the Church's worldwide operations, and review of every single allegation made by Church apostates and other critics, the US Tax Authority IRS issued ruling letters on October 1, 1993 recognizing the tax-exempt religious and charitable status of the Church of Scientology International, the Mother Church of the Scientology religion, and 150 affiliated churches, missions and social betterment organizations - all Scientology-related entities in the U.S. and many non-U.S. entities as well. In this exacting review, conducted under the supervision of the most senior officials over exempt organizations in the government, the IRS concluded that the Church is operated exclusively for religious and charitable purposes.
In issuing its favorable exemption rulings, the IRS necessarily determined that: 1) Scientology is a bona fide religion; 2) the Churches of Scientology and their related charitable and educational institutions are operated exclusively for recognized religious purposes; 3) the Churches of Scientology and their related charitable and educational institutions operate for the benefit of the public interest rather than the interests of private individuals; and 4) no part of the net earnings of these Churches of Scientology and their related charitable and educational institutions inures for the benefit of any individual or non-charitable entity.
The IRS reached its considered and unqualified opinion that the Churches are tax exempt only after conducting the most extensive and detailed exemption examination in its history.
Indeed, the examination was so extensive that the administrative record of these proceedings comprises approximately twelve linear feet. The extensive examination by the IRS included numerous queries into the corporate and financial structure of the Church of Scientology ecclesiastical hierarchy, the religious services ministered to parishioners, the organization, administration and governance of individual Churches, the receipt and disbursement of donations, compensation to ecclesiastical executives and others, and many other matters.
This examination also included the review of balance sheets, bank statements, cancelled checks and similar financial information. In addition to reviewing responses to specific questions, the IRS also conducted on-site examinations of facilities of various Scientology Churches and Scientology organizations, examined hundreds of boxes of their financial records, and thoroughly reviewed their activities. All IRS concerns were fully satisfied by this extensive and rigorous review process. Otherwise, exemption would never have occurred.
The IRS specifically examined details about the Church's fundraising practices relating both to the proselytizing practices of the Church and its policies relating to contributions for services. The IRS has confirmed that they would not have made favorable determinations if they had found that (i) the Church impermissibly served private interests; (ii) it had violated a fundamental public policy. The determinations by the IRS included the finding that the Church of Scientology meets the definition of a "Church" as well as a charitable religious organization.
In the United States, Scientology is officially recognized as a religion throughout the United States government. Ministers of the religion are entitled to minister immigration status by State Department and Immigration and Naturalization Service (INS) decisions finding that Scientology is a bona fide religion. As noted in a 1996 State Department record released pursuant to the Freedom of Information Act, the United States government's position is that the Church of Scientology is as much a Church "as the Catholic Church or any other commonly recognized church".
The State Department's human rights reports each year express concern when there is discrimination against the Scientology religion. The State Department has expressed concern regarding religious discrimination directed at the Scientology religion and Scientologists in certain European countries in human rights reports over the last 12 years.
Scientology - Religious Recognition in Europe and around the World