If you didn't know what it was, I could easily understand that teffilin might look like something dangerous. I think it's great that kids are into religion. After all people don't see religion as important as they used to.
Should flight attendants be trained on every religious practices that might take place on a flight? No. Maybe the kid should have told them that he was going to be praying with the teffilin during the flight.
I do not think that he should have to wait to get to his destination to pray. He wasn't doing anything dangerous. He is obviously observant and this morning prayer with teffilin is important to him. It's not like it was Shabbat and he was lighting candles on the plane (which would not be safe). This act of prayer was harmless. People may be more vigilent and worried when flying but that shouldn't stop people from doing what they feel they need to (with all safety precautions taken).
"How bout a little black dress?"~hannahshule
"I have a penis, not a vagina." ~munkustrap178