The reason is because flammable liquids will not eat through plastic cups. Flammable liquids will eat through styrofoam and the wax that seals plastic cups, hence the allowance to bring them through the walkthrough. Open containers are NOT allowed through the x-ray due to possible spillage. Unopened cans of soda, beer, or whatever drink you happen to have are allowed as they are unopened. Of course this comes from my official TSA training materials, which like my Flash Gordon decoder ring is chock full of interesting material now that I have gotten around to reading through it.

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Don't take life too seriously, afterall, you won't get out alive.