Was this legislation intended to fund non-religious organizations such as the San Diego Padres, or was it intended to fund religious organizations such as churches, synagogues, and mosques?
(1) Religious organizations make their own internal laws, rules and regulations. Congress does not legislate their rules for them.
(2) The Padres are a for-profit organization and are a silly example.
The new legislation was intended to end discrimination against faith-based non-profits. The government already provides funding for anti-religious non-profits like the ACLU, the NEA and Planned Parenthood. The new legislation ends the imbalance.