As the reductio ad absurdum of his argument builds, so too does the pace of the poem in imitation of the sex act.
Everybody had them, even rich people. And furthermore says that although your parents urge you to not get married to me, we already have inside the living soul of the flea. And note the internal rhymes in lines 4 and And in this flea our two bloods mingled be; Wherein could this flea guilty be, What Is The Religious Imagery in The Flea?
Both poems also speak of virginity being very important, especially before marriage because if a woman had lost her "maidenhead" before, the husband would have the right to leave her without the need for a divorce His tone is gentle and romantic. He says that the flea can suck his blood, and then jump to the girls and suck her blood, and share all three of the souls in one body.
Marriage is also one of the seven Catholic sacraments so to kill the flea would be an act of sacrilege, violation.
Using a metaphysical conceit, the poem is written using that relationship in mind, which today most people would see as kind of funny or odd.