"According to the Torah which they [the Sages] teach you and according to the law which they expound to you, shall you act, you shall not turn from that which they tell you - neither right nor left" (Devarim 17:11). "Even if they tell you that right is left and that left is right! And certainly if they say that right is right and left is left" (Rashi quoting Sanhedrin 89). This is what is meant by "Emunat Chachamim" - faith in the Sages. Some people think that faith must be blind and preclude understanding. This is a very shallow interpretation. It allows skeptics to say: "If faith is not a function of the intellect but rather some vague emotion that I personally do not feel, then there is no reason for me to believe." On the contrary, faith is the greatest exercise of intellect and the greatest achievement of philosophy that exists.
Faith in Sages means trust, communication, and a common point of reference. The Halachah speaks of the honor and reverence due to Torah scholars, but "Emunat Chachamim" is on a higher plane, it is a deep, pervasive, vital feeling of connection. Faith in the Sages is an extension of faith in G-d - an extension of our faith in The One Who gave us the Torah - to faith in those who continue to disseminate Torah. "And they believed in G-d and in His servant Moshe" (Shemot 14:31). "Emunat Chachamim" means faith in the Oral Torah, which has been handed down from one generation of Sages to the next, from the very beginning until this day. The Oral Torah is Divine and eternal and a direct extension of the Written Torah. However, it reaches us indirectly, on a more human plane, through Torah Scholars. It makes no difference if they have gained their Torah knowledge through intellectual analysis refined by years of Torah study until their thought processes parallel those of the Torah, or if they have achieved a "Divine Inspiration;" i.e., not something magical or a sudden prophesy, but an enlightened understanding likewise gained through years of Torah study, as it says in Baba Batra 12: "Prophesy was given to the Sages."
There are differences of opinion among Torah scholars, but all opinions are "G-d's living Torah." These opinions are likened to sparks flying from an anvil, breaking into 70 different rays, each one representing another facet of the "70 faces of Torah." All of these combined constitute one great, all inclusive truth. This should be our approach to Torah: To elevate and include all the "facets" of Torah. There are also, however, approaches which are outside the bounds of the Torah. It requires hard work to identify, refine and purge them. There are also approaches outside the bounds of Torah, but which have sparks of holiness, requiring more delicate work to refine.
Therefore, no one should make light of his own abilities, treating his own thoughts, feelings, desires and tendencies as worthless. They are a reflection of the Image of G-d in which he was created. Faith in one's Rabbi does not imply subordination or relinquishing the right to think for oneself. It should rather uplift one's inborn tendencies by refining them, certainly not by forcing them into a mold which is foreign to himself. This process of refinement is painful at first, for one must detach himself from parts of his life which are in reality foreign to him, but to which he has become accustomed, and which become difficult and painful to do without.Faith in the Sages means trusting them. Your connection to your Rabbi depends on your trust, and may be a long drawn-out process. There may be a conflict between the development of your ability to think critically and independently of your Rabbis and teachers, and the deep love and respect you feel for them. These two flames slowly unite into one bright torch.
"Intellectual analysis and a sense of faith and admiration for Men of G-d, the bearers of the great traditions wherein the treasures of the Divine are hidden - [these two approaches] differ psychologically [and subjectively] to a great extent" but "these two forces really complement each other" (Maran Ha-Rav Kook, Orot Ha-Kodesh 1, pp.47-48).
Faith in the Sages should not make one into something he is not, quite the opposite - his faith should help him refine and develop his own unique self tenfold. Sometimes, when one begins a rabbi-student relationship, he relinquishes his own personality as if he was an infant, but this is merely a transitional period until he undergoes a process of self-refinement. He then becomes his own man, able to think critically and freely for himself.