The news peg for this particular story (i.e. why the Catholic Church and not all denominations) is ostensibly the Church's ongoing legal battle and settlements re: clergy sexual abuse, but also the fact that the church's lobbying arm successfully argued an exception for religious organizations to not be disqualified under the rule's dictate "that only businesses with fewer than 500 employees, including at all subsidiaries, are eligible.":

> The Catholic News Service reported that the bishops’ conference and several major Catholic nonprofit agencies worked throughout the week of March 30 to ensure that the “unique nature of the entities would not make them ineligible for the program” because of how SBA defines a “small” business. Those conversations came just days after President Trump signed the $2 trillion Coronavirus Aid, Relief, and Economic Security Act, which included the Paycheck Protection Program.

> In addition, federal records show the Los Angeles archdiocese, whose leader heads the bishops’ conference, paid $20,000 to lobby the U.S. Senate and House on “eligibility for non-profits” under the CARES Act. The records also show that Catholic Charities USA, a social service arm of the church with member agencies in dioceses across the country, paid another $30,000 to lobby on the act and other issues.

Also, the Catholic Church is just fundamentally a more hierarchical and unified institution compared to other denominations. Sure, other denominations have dioceses and bishops, but not as rigidly structured as Catholicism, e.g. cardinals who work directly with the Pope.