"I.. I think it makes a difference."

Although she gets his explanation. She couldn't explain how magic works, just the same way she can't explain exactly how a car manages to move. That does make it very similar. But..

"Magic feels special, after all.." Madoka starts to blush a little, like she's embarrassed to put it this way, but can't really find any other way to put it into words. "I-It feels like something that could make miracles happen."