Although felons are not strictly barred from becoming pilots, the FAA has leeway in denying licensing. Good moral character is an expected character trait of pilots. If you are unsure about your felony conviction, contact the FAA.
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Convicted felons may face travel restrictions that limit their ability to move freely. However, in most cases, felons that have served their sentence can enter other countries, assuming they have a valid passport. There are several exceptions, with some countries explicitly prohibiting felons from going abroad.
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Just like every other passenger, pilots must go through security screenings and follow all security protocols. Different airports have different procedures, but it's not uncommon for pilots to remove their shoes, belts, and any other metal items, and submit to a full-body scan or pat-down.
Whether traveling internationally or not, pilots and flight attendants always carry their passports. Most airlines require their crews to keep their passports with them at work.