Chukas

The Red Heifer is touted as the perfect illustration of “chok”, the decree of the Torah, for it presents the quintessential paradox and internal contradiction. Its ashes purify those who are contaminated while those who prepare it become impure.‎

Rashi comments on the words זאת חקת התורה, this is the decree of the Torah, that the Satan & nations of the world taunt the Jewish people saying, what kind of commandment is this & what's the reason for it? Therefore the Torah labels it a decree for which we have no right to delve into its mysteries. The reasons are divine & not for mortal  ‎comprehension. 

Now, why shouldn't we question the Mitzvos? Wouldn't knowing the reason for the things we do only help to strengthen our commitment to Torah?

The Mishnah in Shabbos says that one may not read by candlelight on Shabbos without giving any explanation as to why not. The gemara later on explains the reason: if one reads by candlelight, one might come to fix the flame if the light flickers & that would be in violation of the rules of Shabbos. 

When Reb Yishmael read this law & the explanation for it, he felt that he could read by candlelight & avoid fixing the flame even if it flickers. He read by candlelight & then inadvertently fixed the candle when it flickered. When he realized what he did, he said "how great are the words of the sages".  ‎Why was it that this is what caused him to praise the words of the sages? Was he merely impressed that their suspicions were correct? 

The Vilna Goan explains that when Reb Yishmael learned the Mishnah, he wondered why there was no explanation given for this law. However, once he learned the gemara & knew the reason, he rationalized that he could take the risk but he failed. He realized how correct the sages were not to offer an explanation for this law. 

This is what Rashi meant when he said not to question the reasons for the mitzvos. Of course one could try to understand the reasons for the mitzvos. What he's saying,though, is not to let your understanding of the mitzva be used as an excuse not to do it. No matter how we deduce the reason, it's a decree which we have no right to question. (Torah treasury) ‎

The main anomaly is that this cow that purifies ‎those that are impure, makes all of those  that prepare it impure. The Rebbe from Lubabitch says that the Torah wants the pure ones, the learned ones, to be prepared to become impure by going down a level themselves in order to purify others.  Just as those that prepare the ashes become impure in order to purify others, so, too, we have to be prepared to go down a level to purify others.

Perhaps Rashi is addressing this as well.   Rashi, himself, tells us the secret to the mitzva of the Red Heifer, for, if you look at the Rashi after the section of the Red Heifer, he states a whole different explanation as to what the words mean, & actually gives a reason for the all the inconsistencies & translates all the words in a totally different way. He compares the Red Heifer to the Eigel, demonstrating how each thing corresponds to the Eigel & atones for the nation's sins of the Eigel. Therefore, the Red Heifer comes to counteract sin.

Even though the pure people need to counteract the actions of the sinners & help them see the light, it has to be done without compromising one’s standards.  This is what Rashi is saying; even though there are perfectly understandable explanations that are rational, yet it's classified as inexplicable to teach us that, even when we think we understand the reason & perhaps feel that it doesn't apply to us, know that the laws of the Torah are a decree not to be questioned, just followed!
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