The line "There is a flower that bees prefer" comes from Part Two of Emily Dickinson's "Nature".
Dickinson makes many different references to the color purple in the poem:
To gain the purple democrat
Of orchis in the pasture
Or rhododendron worn
Not only is the actual color purple used, both of the flowers depicted in the poem are purple in color.
The color purple represents many different things. According to one site, the color purple represents
Purple is the color of good judgment. It is the color of people seeking spiritual fulfillment. It is said if you surround yourself with purple you will have peace of mind. Purple is a good color to use in meditation.
Therefore, the use of the color purple in this poem could reference that it is through the bee's good judgement in which they chose the flower which is purple. The reference to the "purple democrat" could refer to the fact that all bees (as a democracy) choose to prefer a flower which brings about good judgement and peace of mind.
The only other color mentioned in the poem is the color green: "before the world is green." The use of the color green typically symbolizes the spring- a time in which flowers bloom.
Therefore, the color purple represents the good judgement in which the bees use to consider the purple flowers the best.