Flowers are the special symbols of akasha tattva (element of space). Fresh flowers that have been offered to the deity or are offered at the feet of the Sadguru are picked and kept behind the ear as a blessing. This practice has not come into vogue because of the convenience in placing the flower behind the ear or as a safe place which protects the flower from falling down.
The back of the ear is the home for all nādis (subtle astral nerves) that are a cause behind the movement of all the organs in our body. Keeping the flower there is to reduce the heat generated within them and to cool them. It can be said that it is to de-stress them. Thus this flower seated behind the ear sharpens the intellect and reduces the stress on the nādis. However, of late, this tradition is fading away.
-Glimpses of Bhaktimala 4