I was flying on my own at 14 or 15. By that age, the airlines generally don't consider you an unaccompanied minor, so there's no extra charge or paperwork. Make sure your daughter has a photo ID (preferably government issued, like a Driver License, but a school ID will usually work too if she doesn't have her DL yet).
Another thing to make sure of is that she takes all the potentially dangerous objects out of her carryon bag. Even things that you think are probably harmlesss (nail clippers, eyeglass repair screwdrivers, pocket knives, thumbtacks, etc) may be confiscated by the TSA (Transportation Security Administration, the agency that handles all airport security) as part of their Great Pointy Object Search.
As far as the airport experience, it shouldn't be too confusing for a 16 year old. Just make sure to read the signs, and ask someone if the signs are confusing.