When Company A pays an employee money, it's because the employee earned that money.
When Company B pays a health insurance company that provides plan B contraception/abortion pills, it's because the federal government has mandated them to do so.
That is a material difference.
Not to mention, health care insurance is not always fully paid for by the employer. The employee often has to pay a good chunk of the premiums as well. Employees who might have a moral objection to contraception/abortion might have a problem with being mandated by the federal government to pay money to a health insurance company that provides contraception/abortion pills to other people. In essence, they are being forced by the government to subsidize what they believe to be immoral actions.