the message is: "No matter what else is considered a beautiful, you are the only beauty in my eyes"
The poem begun with stating the fact that "The rose is a rose" and that it always was one to begin with, Basically saying beauty is beauty and will always be the only beauty. Then acknowledging that although these other fruits are scientifically beautiful, they look, smell, feel, and are just generally different.
Then the poet says "what will next prove a rose" almost exclaiming that if even these fruits that are nothing alike are technically roses then what else will be considered a rose/beauty. The poet refers to the everchanging beauty standards in society, showing that there are many different things that are beautiful, but from a person to the other each will find their favorite beauty that they believe is true.
In the end, the poet says "You, of course, are a rose" repeating the first stanza but replacing the rose with "you" saying that "you" is a rose of the truest roses, the original rose, that one he saw before all the other ones; "but you were always a rose" he repeats the second stanza and again replaces rose with you. Essentially saying you are a rose but different from the "technically" a rose, but you are ACTUALLY a rose, and you were from the beginning before it has been discovered that scientifically these fruits and other things are also roses.