Not as difficult if you would like to fly from Dong Meung Airport or Suvanaphumi Airport. A now day, many of low-cost airlines provides the flight included the connection to Koh Tao via Ferry, Lomprayah or Seatran Discovery Links.
Nok Air and Air Asia both landing from Donmeung Airport, Bangkok Airway landing from Suvanphumi Airport, Bangkok.
Nok Air and Air Asia are daily Service, you can reserve the flight ticket by your own and then book your ferry ticket with Lomprayah, Seatrans or Songserm. Might check arrival time of flight and departure time of ferry as must easy if you just booking with fly and ferry service. Nok Air is premium low cost airline quite a bit expensive, if your prefer just fly and not need any service recommend Air Asia must best fare.
Tip: Please notes that, if you fly from Bangkok can be tried because time and you might have to waiting for the boat. Recommended! Fly when you are leaving Koh Tao must must better.