I try as well as I can to explain it, I'm really sorry if you don't understand it that's not your fault in any way shape or form, but mine for making it needlessly convoluted. Thanks for your feedback in advance, I will add some more text to explain the Game on my itch.io page as well.
As a small Guide:First you have to do everything the little Animation on the Top right Shows after you've done that. Only click the button once and then wait until you see a note appear out of the flute and you hear the corresponding sound !
The basic idea is that you have certain places in the flute indicated by the colour, as soon as you finished the "tutorial", the flute starts to create notes out of these holes. You have to remember them (they increase each iteration so 1 then 2 then 3 and so on), then you bore into the right Holes (you could bore into others as well that's just more wasted time to remember the right combination), beware not to bore to deep tough or you will destroy the flute ! And then it is just an easy click on the Coloured Indicator and a Note will appear as well as the matching Sound.
If it was correct the same pattern will appear again with another Note added, then you just have to bore and click again on the right coloured indicator hence and repeat this process as long as you can.
Note: 
Coloured Indicator: 