LI charities relieved by 'fiscal cliff' deal

But even if charities' worst fears didn't come to pass, some changes could still hurt, and some people worry that Congress could revisit the idea of limiting charitable deductions as a way of reducing the deficit.

"We're pleased to see that [a cap on charitable deductions] did not pass because that certainly would have had an impact," said Theresa Regnante, president and chief executive of United Way of Long Island, in Deer Park. "We've sort of skated [around] one of the major hurdles."

"It's not as bad as the cap on charitable deductions would be," Diana Aviv, president and chief executive of Independent Sector, a group that represents nonprofits. The group's website gives an example of a couple filing jointly with an adjusted gross income of $400,000 and $100,000 of itemized deductions, including $30,000 in charitable deductions. Under the Pease limitation, their charitable deduction would be reduced by $900 compared to a $6,000 reduction under the scrapped cap proposal.

The estate tax went up by 5 percentage points to 40 percent, but a $5 million exemption for individuals will remain in place and rise with inflation in the future. Aviv said that with a lower exemption level -- it had been $3.5 million in 2009 -- some people would have chosen to give money to charity that otherwise the Internal Revenue Service would have taxed. The higher exemption level diminishes one incentive for charitable giving.

The higher exemption could "cause some of these high-net-worth individuals to leave their family more in their estate than perhaps the charities," Matthew Campo, executive director of Ronald McDonald House of Long Island, in New Hyde Park.

An increase in the highest tax rates -- to 39.6 percent from 35 percent -- raised concerns that higher taxes will leave large donors with less money to give to charity.

"They wouldn't cancel their contributions altogether, but I do think there will be a little pull back from the top," Regnante said.