This is a short poem, and it presents its message succinctly, in a way that is in keeping with that message itself. Jonson is cautioning the reader against the belief that "bulk" or longevity amount to a virtuous life: effectively, he is saying that we should value quality over quantity.
The structure of the poem is interesting: viewed on the page, the narrowing of the poem at the center, where Jonson describes how "a lily of a day / Is fairer far in May," draws the eye. These short lines reflect the short life of the lily, which lives only one day and is "the plant and flower of light," although it only lasts for one day and dies in the same night. The change in line length and meter here captures the reader's attention, underlining the fact that this is the core of the poem. It is upon such "flower[s] of light" that we should focus our attention, rather than upon something which may last "three hundred year" only to fall as a log, worthless.
Man is not made better, Jonson says, by "growing like a tree." It does not represent an accomplishment for us to exist "in bulk," or for a long time, if we are "dry, bald and sere" and leave nothing to show for our longevity. On the contrary, sometimes "beauties" appear "in small proportions," and life "may perfect be" "in short measures." Something which is brief and transitory may leave a far more lasting impression upon us, if it is beautiful, than something which exists for centuries without achieving anything remarkable. It is the quality of a life which is important, not its length.
The basic gist of this poem is that there are many beautiful and perfect sights, moments, experiences and memories in life, but, they are pretty short-lived. The rest of the time, life is pretty dull and drab; however, there are those moments of beauty and perfection that we have to draw on during the down times. Johnson compares these moments to "a lily of a day" and how it is much "fairer in May" even though it lives at other moments too, and "it fall and die at night." While it was alive though, it was a "flower of light." It, while it was alive and in its prime, a beautiful and inspiring lily. This is just like our lives--he concludes with the idea that "in short measures life may perfect be," meaning, life is perfect in only short, transient moments that often fade and die.
He contrasts our lives with their temporary perfect moments to a tree that is perfect and beautiful for the duration of its life, for "three hundred year" before it falls "at last" to become an ugly log. So, "It's Not Growing Like a Tree," refers to how our lives are not constantly beautiful, with perfect moments consistently growing, for centuries. Rather, we are more like the lilies, who have brief but exultant lives of moments of beauty and perfection.
I hope that these thoughts help you to understand the poem a bit better; good luck!