In a sense, the quest for certainty must always, by its very nature, backfire. If you really are certain of something, you have no need to engage in a quest for certainty; thus the quest implies doubt.
Often, this sort of quest is one to replace commonly, but superficially accepted certainties, with a more firm foundation.
Imagine that you were brought up in a homophobic society, and you always believed that gay people were immoral. You decide to put this belief on firm ground by doing research and talking to many gay people. This tactic "backfires" in one sense, in that you will begin to have gay friends and start doubting your earlier prejudices. On the other hand, your new beliefs are based on much better knowledge than your earlier ones, and so, your temporary backwards step of losing an old certainty, involves moving forward to a more secure certainty.
Descartes was trying, in the same way, to replace accepted certainties about knowledge and religious belief with more firm well grounded beliefs.