To elaborate a little bit, NFC is specifically used to refer to standardized hardware conforming to IEC 14443 and specs from the NFC Forum. These devices communicate through very close range tap transactions. In an NFC transaction, you can tell intentionality - e.g. the range is short enough that the user must have brought the device(s) together on purpose. Passports use this form of communication, and all standard mobile payments do as well.

There are also a lot of cards based on IEC 14443 that are technically not NFC: most transit cards are based on Mifare Classic or Mifare Ultralight, proprietary technologies developed by Phillips, now spun off as NXP. This difference is pretty irrelevant for the average consumer - pretty much everyone refers to Mifare cards as "NFC" these days, and I think those card standards may even have been adopted by the NFC Forum to make it official.

In practical use, NFC is not normally referred to as RFID anymore: that term is reserved instead to generically describe a wider range of technologies that don't require close proximity. A great example of RFID is the NEXUS card, which is detected by giant readers that can find the cards anywhere in the general region of your car window. Another good example is replacements for UPC bar codes in products - imagine waving a reader at a pallet of products in a warehouse and identifying all of them.

Quite complicated!

Back to the topic on hand, the TSA readers almost certainly have a 14443-compliant NFC reader of some sort embedded in them for e-Passports and possible future ID cards. They may not even be active, but all that's necessary for Apple Pay to "wake up" is for the reader to be wired up electrically to trigger a Card Present message to the phone.

I suspect Apple will end up fixing this eventually by suppressing Apple Pay when a Passbook boarding pass is visible on screen...