To understand Bradstreet's short poem "An Apology," we need to know that Bradstreet, probably beginning sometime in the 1630's, had been working on one of her longest and most ambitious poems, The Four Monarchies, a survey of ancient history in which Bradstreet intended to show how barbaric life was before the Christian era.  She began with a review of the Assyrian kings and went through the Romans to about 600AD.  At this point, she seems to have tired of the project but picked it up and was trying to finish the poem in the mid-1660's.

Unfortunately, as she recounts in "An Apology,"

My papers fell a prey to th' raging fire./And thus my pains (with better things) I lost, which none had cause to wail, nor I to boast.

She refers here to a fire in 1666 that burned her house and most its contents--including the last part of The Four Monarchies--but, as we can see, Bradstreet's tone in these lines is gentle, and the humor is self-deprecating.  Acknowledging that she had lost interest in this poetic history, she says that the loss is nothing to cry about.

Bradstreet's characteristic very dry humor comes out in the last three lines:

Although my Monarchies their legs do lack:/No matter is't--this last, the world now sees,/Hath many Ages been upon his knees.

She notes in the first line that the history of the monarchies is incomplete and, then, like the good Calvinist that she is, takes a swing at Roman Catholicism: the world can now see that the last monarch, the Pope, has been on his knees for a long time.  Bradstreet is gently commenting on the Pope's (and, by extension, the Catholic faith's) weakness (the have no legs on which to stand) and using the Catholic ritual of kneeling (in which there are no legs) to carry both the joke and the criticism.