Finding Peace in the Darkness - Mark 6:45-56

Why isn't "he" capitalized in scripture when it refers to Jesus?

This article on Bible translations and the use of capital letters is very helpful.  You can find the original article here.

Some Bibles do not capitalize certain pronouns because their translators felt that doing so was not an accurate translation of the original language. The decision to capitalize or not capitalize pronouns is a question of translation, and is not a statement of disrespect. 

For example, here’s a note from a translation consultant for the NIV addressing this question:

The NIV and some other contemporary translations do not capitalize these pronouns for a very good reason: they are not capitalized in the original. The Greek does not use upper case in employing these pronouns, and Hebrew uses only capital letters and has no lowercase letters.

The translators had to face a difficult issue and thought about it long and hard. On the one hand was the practice of showing reverence for God in keeping with the common English usage, and on the other hand was their commitment to providing a precise rendering of the original with no bowing to what was not in the original text. In the end they decided that fidelity to the original was their highest criterion.

While we may not like the absence of those uppercase letters, we can respect their total commitment to the precise rendering of the original.
--Biblica, Publisher of the NIV