You control the quality of your tone through your embouchure and your breath. There are other factors - the qualities of the flute you are playing, for example - but the primary areas where you control the tone are embouchure and breath control.
- Embouchure
- Embouchure is the position of your mouth in relation to the flute's headjoint.
Here is a page that has checkpoints and exercises for developing a good embouchure. - Breath
- How well you use your breath affects every element in your flute playing.
Here is a page that describes the use of the breath and provides exercises for developing breath control. - Vibrato
- An important element in expressive flute playing is use of vibrato.
Here is a page that discusses varying approaches to vibrato, provides some exercises for developing vibrato, and includes links to some valuable resources for developing vibrato.