That incident was caused by unfortunate racial stereotyping; this is caused by a literal interpretation of the letter of the law that hasn't caught up with the times.
This happens because the US is turning into a police state where everyone thinks they've got the right and duty to destroy someone else's live if they don't like something about them (race, religion, sexual life, ...), and the authorities are not only OK with that but actively encourage it to promote constant fear amidst population. If they can charge you with anything at any time and destroy your life, you're going to be a good sheep.
I can certainly imagine tolerance to things that look like bombs or even that simulate bombs in every meaningful way other than explosion.
"Zero tolerance" for bombs and weapons hasn't generally meant that bombs and weapons are not tolerated - that was already the case. Instead, it has meant that things that merely evoke the image of a bomb or weapon are met with intolerance.
For example, I imagine you came across this story:
"things that merely evoke the image of a bomb or weapon are met with intolerance": I call it fear...
The deaf boy story is amazingly stupid too. It seems to me we've put to many people in a position to restrict others liberties/rights, and now we pay the price of stupid "rules" or interpretations of "rules". When you give someone a uniform (it's an allegory), you give him power, which must be handled with care... and intelligence.
I see all this as a lack of intelligence/common sense.
That incident was caused by unfortunate racial stereotyping; this is caused by a literal interpretation of the letter of the law that hasn't caught up with the times.