I can't see an explanation in the Daily News at all, but here's the Washington Post:
Under this proposal, objecting nonprofits will be allowed to offer employees a plan that does not cover contraceptives. Their health insurer will then automatically enroll employees in a separate individual policy, which only covers contraceptives, at no cost. This policy would stand apart from the employers larger benefit package.
...
Last February, the Obama administration announced an accommodation to faith-based nonprofits: A third-party insurance company would cover the cost of contraceptive coverage.
...
Under the policy proposed Friday, self-insured plans opting out of contraceptive coverage would notify the company that administers their health benefits. That third-party administrator would then be responsible for arranging separate individual health insurance policies for contraceptive coverage from an issuer providing such polices.
Insurers who create these plans for self-insured companies will receive an offset from the federal government: Lower fees to sell plans on the new health exchanges run by the Obama administration.
http://www.washingtonpost.com/blogs/wonkblog/wp/2013/02/01/the-white-houses-contraceptives-compromise/
So for employers that use an insurer, this is still the same (since contraceptive coverage pays for itself by vastly cutting the pregnancies and healthcare associated with that, an insurer will be willing to do this). The self-insuring Pharisees, however, are laughing all the way to the bank; they get to parade around their 'moral objections' to contraception, while being saved the costs of so many pregnancies. And the government effectively pays for the contraception instead.