What does the following quote, from The Secret Life of Bees, mean? "When I looked up I saw a crop duster plunging his little plane over a field...

Lily does not feel in control of her own life.

Lily has always related her life to nature.  When she was little, she would feel comforted by the bees that came into her room.  The bees fascinated her, and made her feel part of something bigger.  To her, the bees and nature itself meant that the world was a place of beauty.  Nature was her escape from a pretty terrible life. 

I watched their wings...

Lily does not feel in control of her own life.

Lily has always related her life to nature.  When she was little, she would feel comforted by the bees that came into her room.  The bees fascinated her, and made her feel part of something bigger.  To her, the bees and nature itself meant that the world was a place of beauty.  Nature was her escape from a pretty terrible life. 

I watched their wings shining like bits of chrome in the dark and felt the longing build in my chest. The way those bees flew, not even looking for a flower, just flying for the feel of the wind, split my heart down its seam. (Ch. 1) 

Lily has never felt in control of her life.  From the time of her mother’s death, her father has tyrannically domineered her existence.  When Rosaleen is attacked trying to vote, Lily breaks her out of the hospital but really has no plan.  She just wants to run away, and perhaps find out more about herself in the process.  

In your quote, Lily sympathizes with the insects whose fate the crop duster seals.  She also feels like her life is on the edge of an impending doom she can’t explain.  While it is true that they are on the run from the law, or at least Rosaleen is, Lily does not feel completely free.  Like the insects about to be killed by the crop duster, she worries that she is walking both of them from the frying pan to the fire. 

I spent the next mile in deep worry.  I had no plan, no prospects of a plan.  Until now I’d mostly believed we would stumble upon a window somewhere and climb through it into a brand-new life.  Rosaleen, on the other hand, was here biding time till we got caught. (Ch. 3) 

Lily is quite naïve.  She hoped that the Civil Rights act would make things fair for Roseleen.  As a white teenager, she really didn’t understand how the world worked.  As difficult as things are for Lily, they will always be much worse for Rosaleen.