Can you roll your R's?  Then you can flutter tongue.  The toughest thing about flutter tonguing besides rolling the R is focusing with all that vibration going on in your mouth.  Grip more firmly with your lips so they don't vibrate along with your tongue.  If you work at this carefully, you will find you can flutter tongue even down into the low register. 

If you can't roll your R's (some people can't, it's genetic just like whether you can curl the sides of your tongue) then you have to try another technique.  Make a growling sound in your throat and then blow into your flute.  This will make almost as good a flutter tonguing sound as rolling will.