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I have never been raped at an air port or even patted down. The way things are now are for the best. If everyone traveled correctly, we wouldn't have issues and the lines would move much quicker.
As far as security at subway stations 24 hours, it isn't needed. The only people who get robbed on the subway are the people who flash their i phone or expensive gadget and the people drunk coming home from the bar. If you know your surrondings and are aware you will be at anytime of night. Whenever going back to my apartment drunk at 3am-4am, I take a cab all the way to the Bronx. If it is close to 5am, I will just wait for the Metro North and take that. If you don't think the subway is safe, you have other options.