May a 501(c)(3) nonprofit use general funds raised from donations to support the operations of a for-profit subsidiary operating discount stores (operating daily)?
Assuming that the charity is the sole shareholder of the for-profit subsidiary, there is no federal tax law that prevents the ownership or subsidy. Your question does not make clear whether this support is necessary merely during a start-up period or is anticipated long term. My major question is why you would want to do so for any extended period of time. If the for-profit is mission-related, you might be able to operate it as part of your nonprofit operations and not worry about tax issues. If it is not mission-related, it ought to be throwing off enough profit to make it worthwhile.
If the for-profit is established in order to attract for-profit investors, depending on the form of the entity, you may have unrelated business income issues (See Ready Reference Page: “IRS Says Charities Must Control Joint Ventures.”), or may be questioned if you are using your donations to provide private benefit to the for-profit investors.
You should also be aware that if you are a Pennsylvania nonprofit, there is a statute that I think is unique in the country that allows a small business organization to enjoin unfair competition by a charity that is subsidizing a commercial business that is not within the charity’s exempt mission. (See Ready Reference Page: “Act 55 Defines 'Charity' Eligible for Exemption.” and Nonprofit Issues®, 1/16/10.)