The proper position for the right thumb when playing the flute can be tricky to figure out. There isn’t a one-size-fits-all solution because what works best for a player will depend on the size of their hand and the length of their fingers and thumb. But the end goal for all players is the same: a hand position where our fingers can move quickly and efficiently and the right arm is in as natural a position as possible.
Novice flute players often have issues with the correct placement because we teach them to play using the left hand fingers first - the right hand gets largely ignored and students get into the habit of putting the right thumb just about anywhere to hold up the flute. In my experience with students I have taught, it often ends up too close to the foot joint, close to the pinky.
For most players, the ideal position is to have the thumb beneath the index finger (the f key), give or take a few centimetres in either direction, resting on the fleshy part of the thumb as opposed to on the joint. For some players, a device called the Thumbport (by Solexa) can work wonders for the thumb position and can free up the right hand fingers immensely as well as increase stability when moving from C# to D.
Check out this video where I go into more depth about how to figure out the proper position for your right thumb as well as how to use the Thumbport.