Direct debit payment processing is less expensive than credit card processing. Instead of taking a fixed rate plus a percentage of each transaction (like credit card processing does), ACH only takes a flat fee. The flat fees for both are usually around the same amount.
For example, a common credit card fee might be 2.5% + $.30. An ACH fee for the same amount might only be $.30.
Over time, the savings in fees can save nonprofits hundreds if not thousands of dollars a year.