The problem is that many people don't cook the flour thoroughly when using it to thicken a sauce. Raw flour doesn't taste good at all, plus it makes for an odd texture. What many uninformed people do is simply add raw flour to thicken a sauce, and therein lies the problem. I'm sure that Bourdain wouldn't object to a sauce thickened with a properly cooked roux.

If you need to thicken a sauce and don't have roux or the time to cook the flour until it's done, you can use arrowroot or cornstarch, both of which cook very quickly and don't require the precooking that rouxs do. However, each has its own qualities--cornstarch in particular is shiny and translucent, flour is more opaque and and dull looking.

Sauce thickened with raw flour just doesn't taste very good. To me, it tastes like uncooked dough.

A lot of recipes call for the cook to use a beurre manie - equal parts flour and butter, incorporated - to thicken the sauce. I prefer to cook the beurre manie first. Put it in a small sauce-pan and cook it for a couple of minutes, until it starts to turn golden - I guess this may technically be a roux, it's just not what I think of as a roux - then whisk in a little bit of the sauce. Once it's all incorporated, whisk the mixture into the main sauce.

This is basically how Julia Child does bechamel in The Way to Cook, but I use it for any sauce or broth that needs thickening.