And all the Muses still were in their prime, When, like Apollo, he came forth to warm Our ears, or like a Mercury to charm !
Lines 44 - 46 describe the effect Shakespeare had on drama through a simile comparing Shakespeare to the Roman gods Apollo and Mercury.
Apollo was famous for playing the lyre (hence the warming of the ears) and Mercury was the god of eloquence; by comparing Shakespeare to these two, Jonson is complimenting both the poetic quality (music) of Shakespeare's work and also his skilled use of the language.
Line 44 might seem like a throwaway intro lines 45 and 46, but to us it might be the most interesting of the three. By mentioning that "all the Muses still were in their prime," Jonson is stating that the great age of literature was not back in ancient times when the famous Greeks and Romans were writing, but now, in England, with Shakespeare. This is a pretty profound statement when you sit down and think about it, and one that conveniently places Jonson's lifetime squarely in the middle of the greatest literary age to date.
Nature herself was proud of his designs, And joyed to wear the dressing of his lines ! Which were so richly spun, and woven so fit, As, since, she will vouchsafe no other wit.
Lines 47-50 contain an extended metaphor, which personifies Nature as a woman and compares the act of a woman getting dressed in fine clothes to the poetry and prose written by Shakespeare.
It's easy to imagine a woman getting dressed, but somewhat harder to wrap your head around the idea of nature wearing poetry. This makes Jonson's decision to use the metaphor a good choice, but that doesn't mean the base of his comparison doesn't require a little extra speculation.
Think of it like this: you, a poet, have written the most beautiful description of a tree that has ever existed. It probably goes something like "The tree was clothed in a cloak of emerald leaves, its crown a golden circlet forged from dappling sunlight" except that it's way better than that. The idea being expressed by Jonson is that Nature (who, remember, is personified and therefore gets to have opinions) is proud of the way you/Shakespeare have taken something in the natural world and described it so beautifully. Because your description has been written and is so awesome, then, all trees now get to "wear" it (because now, when people see a tree, they'll think of it as wearing a cloak of emeralds instead of looking at the tree in their own terms, which may be something more like "it's got green leaves, pretty tall, big trunk").
Essentially, Shakespeare has taken something ordinary and common (nature, everyday life, the human experience) and dressed it up by writing about it in such a beautiful way. In other words, Nature with a capital N becomes more attractive when described by Shakespeare, just like men and women tend to look more attractive when they're dressed up for a black tie dinner than they do when they roll out of bed, unshowered and hungover, the following morning.
We move on to line 49 and Jonson is still running with this whole woman's clothes/Shakespeare's poetry comparison. Here, he compares the vocabulary and descriptions in Shakespeare's plays and poems to richly spun and tightly woven fabric (read: expensive, the good stuff).
Line 50 takes the comparison one step further; Shakespeare's stuff is so good that Nature is now no longer interested in the work and descriptions of any other poet (or "wit").
There's also a bigger picture to consider here, and that is the question of art versus nature, or in modern terms, the nature versus nurture debate (as it applies to artists).
This, folks, was a Huge Deal in Jonson's time. It's how many people describe the difference between Shakespeare and Jonson, and it's also discussed in many of Shakespeare's plays, so it's very fitting that that it would have a place in this poem.
See, Jonson is complimenting Shakespeare's natural-born ability for good writing. So Shakespeare was destined to be a good writer because the words that come out of his mouth/pen are just naturally awesome. Nature is "proud" of his designs because nature designed and intended Shakespeare to be a writer, Shakespeare himself had nothing to do with it.
We'll pick this debate back up in a few lines, so if that didn't quite answer all your questions, don't worry—there's more to come.