Credit card processors / merchant acquirers pay out most of their revenue to the following sources:

• The banks that issue credit cards and debit cards (called interchange)
• Visa and Mastercard (called assessments)
• The actual cost of processing a transaction, doing underwriting, customer support, etc.

Processor markup is basically the gross margin of the credit card processor.   Sometimes they disclose how much they are making on top of interchange and assessments (called interchange plus pricing) and sometimes they do not (ERR Pricing, Tiered Pricing).  Full-disclosure, interchange plus pricing is better for business owners.

Processor markup is important because it is the only part of your credit card processing fees that is actually negotiable.