There was a quote in the article that they were prepared to fly commercially. I kid you not. To Afghanistan no less.
Most people don't read past the headline on these articles so they didn't see that part and don't know that Pelosi is claiming her safety was compromised by the President canceling the flight because in doing so he said she was going to visit the troops and therefore her alternate plan to fly commercial would mean she'd be at risk with everyone knowing where she was headed. The joke being, as you pointed out, that she would fly commercial anywhere, let alone to Afghanistan.