The order is affecting plans for nonstop service between Moline and Washington.
Lawmakers last year approved state subsidies for the airport to help cover revenue guarantees offered to an airline. The subsidy was $1.5 million per year for three years.
Rauner spokesman Lance Trover says that spending is under review.
Democratic state Rep. Mike Smiddy says it's a "hiccup" in the plan. He says area legislators and the business community need to work with Rauner to make sure the flight is a priority.