Doctor Faustus ends with the title character being savagely ripped to pieces by evil devils before his soul his dragged down to Hell, where it will spend eternity in the company of Lucifer and all his vicious acolytes. It's not a pleasant ending, to be sure. It may also strike us a tad unfair. After all, Faustus, though undoubtedly foolish and arrogant, was not a completely wicked man, so perhaps he didn't really deserve such a gruesome demise.
But whether one likes it or not, there's no doubt that the ending is an appropriate one from a dramatic standpoint. Doctor Faustus is a morality play, which, among other things, means that it endeavors to teach the audience a certain message. In this particular case, that message, delivered explicitly by the Chorus in the Epilogue, is that we shouldn't turn our backs on God and mess around with the forces of darkness. Otherwise, there is every danger that we will suffer the same grim fate as Faustus himself.
So even if we find Faustus's death unnecessarily gruesome, we should still bear in mind that there's a dramatic logic to the manner of his death. Faustus turned away from God, which in Marlowe's day was a very serious matter indeed. Not only that, but he made a pact with the Devil in return for power, wealth, and extraordinary magic powers. In late sixteenth-century Europe, when the play was written, this was about as serious a sin as it was possible to imagine. And so it's only right and proper that Marlowe should present the consequences of rejecting God and embracing the Devil in the starkest possible terms.