"I am bothered by a certain aspect to the approach that we are taking as rationalists... We analyze our religion rationally only within the acceptable area. For example, we will never entertain the idea that our religion is fabricated and that it is all for naught because that would violate a tenet of our religion. However, in an analysis of history or science there are no walls that are taboo to cross. Why should our analysis of our religion be limited by boundaries if we seek truth? As rationalists, if we were G-d forbid presented with evidence that our religion got it all wrong would we not be forced to accept it? I guess I am struggling with the fact that unwavering belief in anything is not truly rational."
It's difficult to deal with such a topic within the confines of a blog post. I will touch on related aspects of it on other occasions. But I want to make a start, and hopefully thereby be able to clear several emails from my inbox in one fell swoop!
In my view, although some of the Rishonim applied the rationalist approach to Judaism without limitations, we cannot do so. This is for both practical and theoretical reasons.
Practically speaking, there is considerable conflict between 21st century academic scholarship and 21st century Orthodox Jewish ideology. I'm not talking about matters such as evolution, which are not at all theologically problematic; rather, I am talking about the much more difficult challenges from Biblical scholarship, philosophy of religion, archeology and so on. Now, some people consider those challenges to be without merit, or to be outweighed by historical or other arguments in favor of Orthodox Jewish ideology. But others see there as being serious problems here. They either choose to live with the difficulty, or have to significantly modify their understanding of Judaism to suit it, in a way that might be satisfactory for them, but is unsuitable and/or unacceptable for wider Orthodox society.
I don't see this as reason to entirely discard the rationalist approach. Besides, it's just not possible to do so; you can't make people shut their minds off, and Judaism does not expect people to do so. The rationalist approach is well-grounded in tradition and is of great value in how we relate to Torah and mitzvos. Nevertheless, I think it should be accepted from the outset that there can be limits to this approach.
On a theoretical level, I think that there is an irreducible conflict between the very nature of emunah and rationalism. Perhaps there can be a rational basis for faith (depending on how one defines those fundamentals). But if rationalism means that beliefs are always subject to re-evaluation based upon the open-minded evaluation of new evidence and arguments, then I don't see how this is compatible with emunah, which requires absolute commitment to God and does not even permit one to seriously consider alternatives (although, as Rabbi Norman Lamm argues in Faith & Doubt, a certain degree of doubt may be acceptable; emunah being loyalty-to rather than belief-that). Frankly, I think that many Jews today have been dangerously misled by Discovery-style presentations and books into thinking that Judaism unequivocally requires emunah to be based only on logical, scientific considerations; and they have been likewise misled into thinking that religion only has legitimacy and value if based on such methodology. Sure, the rationalist Rishonim thought that, but we're not living in 13th century Spain anymore, and it was rather an aberration in that regard.
All this is in reference to ideologies and approaches, not to people. There are, inevitably, people who attempt to apply a rationalist approach all the way. Some of them believe that the results support the tenets of emunah. Others believe that they do not - which itself does not necessarily mean anything about whether and how they continue to live their lives as Orthodox Jews. More on that topic on another occasion.
(See too this post: Drawing the Line: Is Rationalism Futile?)