The besieged town is the dominant symbol in the poem, and it's a confusing one. The speaker likens himself to a town that has been taken over, but he wants God to attack the town in order to capture it. Actually, if we're being technical, when the speaker says he's "like an usurp'd town," he actually makes a simile, but by using the simile throughout the rest of the poem without making an explicit comparison elsewhere, we can safely call the whole thing an extended metaphor.
So, aside from the request that he be attacked (if he's the town, is it really such a good thing if the town is assaulted?), there's also the confusion about who "usurped" this town in the first place. We might think it's the "enemy" from line 10, but that's not helpful because we don't know who the enemy is, unless it's just that general enemy of God, Satan. The real problem, as we see it, is the line: "Reason your viceroy in me, me should defend, / But is captived, and proves weak or untrue" (lines 7-8).
First of all, why is reason described as a viceroy, when the speaker just compared himself to a captured city? Wouldn't that make reason the force in control of the town (since a viceroy is a local ruler)? And, if reason is in charge of the town, does that mean God is the one who usurped the town, since reason is God's viceroy? Or, is reason the original viceroy of the town, before the town got captured? Either way, it's interesting how the speaker sets up his desire for more attention from God as a battle in which God fights against him. The whole thing is a bit confusing, but it could be intentional, working well with the theme that the speaker doesn't really know whom he's addressing (see "Lines 1-2" in the "Detailed Summary").