Knowing that ultimately it is to our benefit to fulfill every mitzvah, whether we understand it or not, doesn’t necessarily mean that they are being done for selfish reasons. Just as knowing that there is reward and punishment for our actions doesn’t preclude doing them (or avoiding the “no-nos”) for the right reason, knowing that everything G-d does and commands makes sense doesn’t mean that we must be doing them for the wrong reasons.
Trusting G-d, and therefore following Him “blindly,” i.e. doing things we wouldn’t have otherwise considered doing, is not the same as “blind trust.” The latter, often referred to as “emunah p’shuta” (blind faith), isn’t based on assessing the different possibilities and concluding which religious system is most likely true. Rather, there is a starting point of faith (usually based on how the person was raised), with that faith either never being tested by considering any other options or it being adopted in order to avoid doing any heavy thinking about it. It is the person’s default religious setting. On the other hand, trusting G-d because of His track record (i.e. other commandments or the flow of history), and/or because it makes more sense for there to be a Higher Power with a Higher and Greater Intellect, often called “emunah al pi chakirah” (faith through reason), is achieved through careful consideration of the possibilities. Throughout history there has been a long discussion about which one is preferable.
When we are young, it is clearly advantageous to be taught to have “blind faith,” as the young mind can not always grasp the concepts needed to make an informed decision. We therefore do not teach our children other religious options and why we think ours is best, but try to give them a foundation in our faith that will help them make an informed decision when they are older and better equipped to grapple with things. One of the major disadvantages of continually searching for religious truth is that it expends valuable time and resources that could be spent growing within the specific faith system; these resources would not be well spent on such a search at that age anyway. Although intolerance often accompanies thinking that there is only one real possibility, when the ability to think three (or four) dimensionally (hopefully) develops, an understanding as to why others may have made different choices usually develops along with it.
As we get older, things that used to appear as black and white start to become shades of gray. However, gray is nothing more than tiny black dots and tiny white dots that only appear gray because of an inability to “zoom in” closely enough to see the individual dots; it is our responsibility to learn how to distinguish between them so that instead of seeing gray we can tell where the black is and where the white is. Nevertheless, until we gain that ability (and each “gray area” demands a specific expertise to be able to make such distinctions), things that had been assumed are no longer certain, and we must choose between embracing the challenge of reexamining the faith of our youth or embracing the faith of our youth and ignoring the challenges. There are several possible reasons to embrace the challenge, including having the desire to know and understand the truth or having the desire to be able to rationalize a weakening commitment to the faith. With the advent of the internet, both desires have become much easier to pursue. The exact same challenges are sometimes presented as questions designed to spur a conversation that will hopefully lead to a better understanding of the issues, and sometimes presented as questions (or statements) designed to erode religious commitment. Some have resorted to a minimalist perspective in order to avoid having to become engaged in these challenges, while others are working through these challenges, either privately or publicly. The more confident one is in the belief system, the more likely it is that a sincere attempt to resolve any difficulties will be made.
While some are content to remain confident in their own belief system, choosing to spend their time and energy focusing on their spiritual growth within that system, others recognize that members of many other, mutually exclusive, belief systems are just as confident in their own faith. This realization often leads to comparing (what we know about) other belief systems with ours in order to justify the confidence we have in our own despite others having the same confidence in theirs. (Atheism qualifies a belief system too.) If this comparison is just a superficial one, done to rationalize our “blind faith,” it is of little value. In any case, once we go beyond “I just believe” to “I believe because,” we have left the realm of “blind faith.” The only question is how much time and effort we are willing to commit to finding a solid rational basis for our faith. The Torah itself instructs us to compare our belief system with others (D’varim 4:6-8 and 32-34); it would be difficult to suggest that we are only supposed to do so half-heartedly. However, the more time and effort spent understanding why we should continue to commit to a Torah lifestyle, the less that is left to delve into the nuances and beauty of that lifestyle. There must be a balance between how much time is devoted to each, although very often understanding the underpinnings of our religion will greatly enhance our observance of it.
The Or HaChayim and the Kli Yakar discuss why the Torah says “zos chukas haTorah,” “this is the difficult-to-understand law of the Torah,” rather than “zos chukas hatumah” or “zos chukas haparah,” which would refer more specifically to the laws of spiritual impurity. Any sincere search for truth must be accompanied by a realization that we are limited beings, and cannot expect to understand everything. This was the upshot of Sefer Iyov, that only G-d has full and ultimate knowledge. Not being able to fully answer every challenge should not erode our trust in the religious system, especially if a sincere search leads to the conclusion (to be subsequently revisited, time and time again) that it is the most reasonable approach to life, how it started, and how to live it.
We place our trust in G-d regarding mitzvos we don’t understand; the same can be said regarding theological challenges. “Zos chukas haTorah,” this applies to the entire Torah. We can fully commit to G-d and His Torah even if we don’t have all the answers (yet; I know several people who lived with their questions for years, and were eventually able to resolve them). As long as we make a sincere effort to find the truth, we can be confident that G-d will help us do so.