this is completely ridiculous, but not nearly as common as people seem to think. until i took this trip to kazakhstan, i think i have traveled with arabic flash cards and/or other materials in arabic on every flight i have taken since 9/11. almost all of those flights either began or ended in philadelphia international airport. i have never had any problem at all.
at times my arabic studies have produced an interesting conversation on the flight, but otherwise my games of "spook the air marshal" are more of a joke than anything i really worry about. i've even been picked out of line for random, more intrusive screening. notwithstanding my incriminating copy of hans wehr in my carry-on, i have never experienced any special delays.
still, i realize it does happen to some people some times. but for every daniel rubin that makes headlines there are a ton of people who do not have an idiot for a screener. they pass through security on their merry way even with things in their bag that are printed in a funny script.