Elsewhere in the tax debate, many charities are choosing to stay on the sidelines when it comes to the estate tax, because lawmakers are unlikely to be swayed on that issue. Republicans’ wish to repeal it would depress charitable bequests, which are tax-deductible.

Other policy questions in the nonprofit sector could emerge, including tax rules for foundations and limits on political activity by churches, and those could divide charities.

What unites them is protecting the income-tax deduction.

“It’s really the heart and soul of our sector,” said Vikki Spruill, president and chief executive officer of the Council on Foundations, an industry association. “As government resources become more scarce, philanthropy will not be able to fill the gap, and so we are concerned that we might have sort of a two-pronged problem.”

David L. Thompson, vice president of public policy at the National Council of Nonprofits, said charities aren’t “telling Republicans not to do what’s orthodoxy.”

“Our message is, those policy decisions have consequences,” he said.