That’s what the ruling did. It decided that the business can decide to withhold medicine to their employees (HBC, IUDs, Plan B, etc) on the basis that the business owners' religious convictions are more important than the desires of their employees to control whether or not they get pregnant. Many of those people are gonna be from religions that are 100% okay with birth control. Their religious freedom is moot in the face of what corporations want. The people who work for those businesses are absolutely the ones getting screwed over.
The thing about employer-provided health benefits are that they’re essentially part of your payment. The business takes some money out of your paycheck and pools it together with the other employees and gives you health insurance from that. Sometimes the business pays for part of it, too, but that’s also essentially a form of payment to you, hence why they’re called benefits. They’re meant to be an incentive for people to work for you. But a business deciding that you don’t get access to certain medications (and seriously, people, birth control is a necessary medication for so many people for so many reasons!) is them deciding for you how your money should be spent. It’s not their money. It’s meant to be part of your wages.
Now, I actually think it’s a little strange how, for so many people, our health insurance is determined by where we work, to the point where the system kind of revolves around it, and it’s only very recently that there were any other realistic options for people who can’t get benefits from their employer. Me, for example. I’m self employed for the most part, working part time at a tiny local business that doesn’t offer me benefits. Before Obamacare, I had no health insurance. I much prefer having something independent (though my boss is a pretty liberal woman who I doubt would deny me birth control.) I don’t really think our bosses should be in control of our health. It’s weird and illogical. But so long as that’s how the system works for most people, then employers have to be fair to everyone. Denying people birth control is absolutely sex discrimination, rooted in misogyny and religious bigotry.