For those not from Europe: You don't actually go through a passport check to travel between the Schengen countries (This is almost the whole EU minus the UK). Airlines - especially budget airlines - might sometimes check to make sure you haven't given your pass to someone else, and there will be a security check, but there is no border/passport check (also no e-gates).
Regarding the quote from the article above, that basically means that a lot (almost half) of the passengers are _not_ facing this problem because they are traveling between Schengen countries.
(off topic: great example of one of the benefits of the EU, in my opinion)