"When a Jew falls away from his faith, heaven forbid, there certainly remains some 'dot' of faith within him. The very fact that he feels pain at having fallen away from faith, and seeks good advice on how to restore and strengthen his faith, this in itself is an act of faith. For in the innermost parts of his heart, he truly believes in God and in the holy zaddikim. However, he does not feel this faith openly and fully, for to him faith is in the category of smallness and brokenness. That is why advice will be effective for him, because as soon as he is offered a good suggestion for the enhancement of his faith, he grabs hold of it as if it were a precious stone, for a bit of faith still exists deep within him, and he truly yearns to perfect and elevate his fallen, broken faith. Therefore he can gather several good bits from the broken fragments of his faith and thereby make it whole. This is the equivalent of 'the tablets and the broken remnants of the tablets lay together in the ark' (Brachot 8b). By the very fact that he sees his broken faith as corresponding to the category of the broken tablets, by this alone is it restored."
-R' Nachman of Breslov, Emet Vatzedek, Emunah #40, quoted in N. Lamm, "The religious thought of Hasidism: text and commentary", p. 93.
According to R' Nachman, someone with religious doubts is like an ark containing "broken" or "cracked" tablets from Sinai. This damaged faith is certainly is not as good as unblemished faith, but is still holy. And under the right circumstances, it may someday be mended into the "whole tablets" of complete faith once again. In fact, by simply recognizing that a person's partial faith is real and valuable even if not complete, it can become a sufficient basis for much of his religious life.
(This is certainly not the only passage in which R' Nachman speaks about religious doubt, but it was new to me...)