Exempting religious organizations from taxes on contributions and donations is one thing. Exempting them from capital gains taxes on secular stock investments is another. But the church as do other religious institutions, claim tax exempt status based on the doctrine behind the First Amendment establishment clause.
Yet Catholic dioceses all over the country are filing for bankruptcy protection because of tens of billions of dollars in jury awards against the church for the serial child sexual molestation that went on for decades with the church's knowledge, (which is why they were held liable). In those cases the church asks to be subject to secular bankruptcy laws to protect them from having to pay the billions in jury awards but, claim exemption from tax laws based on the establishment clause.
Adding to the hypocrisy, The Catholic Conference of Bishops has a well funded lobbying effort in Washington, staffed by 350 people whose sole job is the same any other lobbyist -- to influence and even write legislation that gets inserted in bills. In the case of the church, or any religious instituion it is a clear violation of the separation of church and state and a breaking down of the "wall" between religion and the affairs of state that Jefferson and the Founders said the amendment was designed to create.
This is not to say that the church doesn't have freedom of speech, to speak out about issues that matter to them, to support candidates who support those issues and to exercise their right of free speech to influence elections. But influencing elections is one thing -- influencing, lobbying and writing legislation is another.