Two important particular themes are the decline of organized religion and the void left by its disappearance. The two general themes I found are ritual and place.
The speaker is evidently agnostic or atheist. He only goes into the church after determining that nothing is going on. After exploring the church, he questions what will become of churches after religion is no longer useful. The speaker assumes that all others, like himself, will eventually stop going to churches for religious purposes.
At first, his questions are quite practical. What will become of the buildings? Then he wonders if the churches will become symbols of superstition, bad luck, or good luck charms. But he concludes that even those superstitions will eventually die.
The speaker also asks why he, an agnostic, continues to stop at churches. He notes that one should take his hat off in a church. He is hatless, so this isn't necessary. But, although not a reverent man, he does unclip his cycle-clips in "awkward reverence." He is not religious, but he does continue to go to churches (a ritual at a particular place) with a kind of reverent curiosity similar to the religious person who goes to church seeking faith, wisdom and answers.
In the sixth and seventh stanzas, he notes that churches have always been places for significant life events (baptism - birth, marriage, and death). He also notes churches are places for serious thinking. A possible conclusion is that people will always need a place where they can celebrate, affirm or mourn with special significance.
Therefore, he practices one theme of the poem most closely associated with traditional churchgoing: the symbolic power of the ritual. The theme of place is equally important in that, regardless of religion's role in our lives, we seek certain places for certain events. The speaker's reluctant reverence (with the cycle-clips) indicates that, despite his lack of religious beliefs, he wants to have some place where he can come and be serious, a place "to grow wise in," which is why he frequents churches in the first place. Like the traditional churchgoer, although for different reasons, he craves the symbolic power of ritual and place. And this is an answer to his question. Churches may go, but symbolic rituals and places seem to endure.