you can fly to koh samui from BKK via Bangkok Airways and they have a monopoly on that route to the island so be prepared to pay a lot for the airfare.  when i went there last Oct, the airfare from Bangkok to Koh Samui was just as expensive as my air asia ticket from KL to BKK.

you can also fly THAI airways to Suratthani airport.  then take a shuttle transfer (1 hour) to Donsak Pier, and then a 1 1/2 hour boat ride to Koh Samui.....

i don't know whether Pelangi Air still flies direct to Koh Samui from KL....