To start, Herbert seems to propose that evil has divine origin:
That what so universal are, must come
From causes great and far.
Furthermore, in his view, evil is not that different form God: "This Ill having some Attributes of God."
Perhaps what Herbert suggests, ever so carefully, that this could have been God's plan all along... How so? Well, God could end all evil by taking away our free will. By turning us unto automatons, like the animals are.* But God already has animals. He wants us to become good by our own choice. In other words, God, save for taking away our humanity, must leave it to us to end our evil ways.
And to achieve the latter, according to Herbert, all humans must develop their God-given capacity for reason, which would make them only will good: "Exalted Spirit that's sure a free Soul", in Herbert's words. As it stands, however, most people are yet to fully develop their humanity -- and that's why evil persists:
The World, as in the Ark of Noah, rests,
Compos'd as then, few Men, and many Beasts.
* Or angels, by some accounts.
This answer borrows heavily from "The Unsteady Crown: The State of the Monarchy
in Edward Herbert's Poetry of Politics" by Anne B. Mangum.