The rain, like the cloud, comes up over and over again in this poem. It's a really important recurring image. Just like "Heaven" and the "silver sphere," it's associated with the sky and the things that come from it. The speaker wants us to feel that sensation of always being lifted up, following the song of the skylark as it shoots up into the sky.
Line 30: In this case, the rain is a metaphor. The speaker describes the light that comes from the moon as being like rain. The light turns into a kind of liquid, and the sky overflows with it.
Line 35: Now the rain is used as part of a simile. The rain that comes from "rainbow clouds" is compared to the "rain of melody" that comes from the bird. We dig that little internal sound echo in "rainbow" and "rain" too.
Line 58: Here's another lovely quiet little rain moment. At this point, the speaker is just doing his version of "My Favorite Things" (hey Sound of Music fans!), listing things he really likes. Rain on flowers makes the list. It's a setup though, because he's going to tell us that the skylark's song is better than any of that stuff.