I remember having an argument with a classmate of mine back in high school. We were chavrusas (study partners) that year spent a fair amount of time arguing issues that weren't necessarily in the Gemara (Talmud) that we were studying at the time.
One argument in particular that I remember is when he brought up the "halacha" (law) of Eisav Sonei L'Ya'akov (Esau [i.e. non-Jews] hates Jacob [the Jews]). He insisted that every non-Jew hated every Jew because of this "halacha." I, having been exposed to and having been shown kindness by non-Jews in the past, knew that this was bunk (as a "halacha"). Sure, there were non-Jews that hated Jews - no one could dispute that - but that, as a general rule every single one of them hated us? To me that was completely ludicrous; and I told him so. My chavrusa, being far more of a fundamentalist than I ever was, insisted that since it was a "halacha," it had to be true. When I pointed out to him instances of non-Jews saving Jews in the Holocaust (at the risk of their own lives) or even kindness done to me, his response was "well, they were only doing it for their own sakes." No amount of reasoning could persuade him of this.
Then, he threw me the "well, if you and your "friend" the goy were starving and there was only food for one, let's see if he doesn't hate you then?"
At the time I was too young and naive to come up with the obvious rejoinder to that, so I let the matter drop, although I still did not agree with him. But the fact that he was reading a text so literally that it's plain meaning was so obviously false (although, I suppose, if you live a sheltered enough life maybe it's not so obvious) disturbed me. Thinking back, that may well have been the first "crack" in the armor, the first time I questioned either the accuracy of a text or whether the text must be understood completely literally.
Of course, as I grew older and developed critical thinking skills, I began to question the literalness of other texts as well. Moshe Rabbeinu's height; Og's vast girth, longevity and the tale of his survivial of the flood; the stories of Rabba Bar Bar Channah's travels; the stories told of the Ba'al Shem Tov and others; the Geocentric description of the universe in the Rambam, and many, many other texts. I wasn't willing to completely disregard these texts as "fairy tales" or simple embellishments, but simple reason told me that they could not be true on a very literal level. This was further "confirmed" for me when I began to realize that in order for some things l was led to believe to be literally true, not only must the current scientific knowledge of it be false, but there must also be a massive conspiracy covering up the truth - for example, if the solar system was truly geocentric, then not only is the science wrong, but NASA and every astronomer on earth must be actively covering up the truth. While I like a conspiracy theory just as much as the next guy, it simply defies reason to believe it.
That's probably why the whole affair with Rabbi Slifkin's books resonated with me, because this conflict has been a very large part of my Jewish thinking for the last twenty years - and now here it is out in the open for discussion. People are finally coming "out of the closet" (if I may borrow a metaphor) about understandings that they've had for a long time but have been afraid to express for fear of being shunned by the community. And, of course, once the bottle has been uncorked, it's going to be nearly impossible to put the genie back in.
And that gives me hope for the future.