O rose thou art sick (1)
The poem starts out with the rose already sick, but something tells us that it gets infected because of the worm's "dark secret love." That's what kills it anyway, and surely sickness kills plants as well.
Has found out thy bed Of crimson joy (5-6)
A bed? Crimson joy? Sounds a lot like something sexual, doesn't it? But something about these lines screams forced entry, even rape.
And his dark secret love Does thy life destroy (7-8)
"Dark secret love" can be read as a sexual reference. We often associate darkness and secrecy with physical intimacy, but the darkness here is strangely unromantic. It's associated with the destruction of the rose. The poem doesn't say sex is bad, but rather that it's bad if it's done secretly in the dark. Does that mean sex should be public? Not necessarily, but "dark" and "secret" isn't the answer either.