Here's the issue: on January 20, the Director of Dept. of Health & Human Services issued a press release stressing that "scientists have abundant evidence that birth control has significant health benefits for women and their families." Therefore, she argues, religious healthcare providers must give "women with health insurance coverage ...access to the full range of the Institute of Medicine’s recommended preventive services, including all FDA-approved forms of contraception."
Catholics say they don't believe in birth control (though almost all actively use it) and shouldn't be made to have it available for people who seek medical care at their facilities. Unfortunately for them, medicine is a matter of fact and does not change despite what one might choose to believe. People who are not Catholic will make use of these facilities, and as medical providers these Catholic institutions have a responsibility to give these people the highest quality care in every respect.
Since this is apparently a difficult concept for some to grasp, I have included an informational diagram.
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More interesting still is the way the right wing media has portrayed this decision as an official declaration of war on religion as a whole by President Obama. There are a number of issues with this, the first being that it implies the president played a direct hand in the decision making process of the Department of Health and Human Services - a large bureaucracy staffed by thousands of medical professionals and career administrators. It would be obvious to anyone who has studied how the executive branch actually functions that the president does not micromanage such decisions.
The second and most important issue with calling this the beginning of Obama's "War on Religion" is that it hasn't even been a week since President Obama spoke publicly about his faith at the National Prayer Breakfast. After this speech, the president was roundly criticized by conservatives for using New Testament quotes about poverty and charity to frame his reelection campaign.
Yes, you read the correctly. The right wing media is simultaneously criticizing the president for declaring war on religion while attacking him for his professed Christian beliefs. It is a crystal clear illustration of the absurd double standard we have in this country where Christians claim to be persecuted when they are denied special privilege. This is why our cause is important. This is why we fight.