As any religious scholar will tell you, Christ said many things that were profound, inspiring, and uplifting, but He wasn't all too entertaining... It's an interesting phenomenon: Jesus is generally presented as an admirable figure, or at least benign, even in non-Christian or -Christian media.
Atheists, Jews, Buddhists, cynics—anyone who might author stories unflattering in their portrayal of the Almighty, The Bible or religion in general—are nonetheless complimentary to that Nice Jewish Boy. to Christianity ("Jesus was cool even if his followers all suck"), but also as a Pet the Dog moment from a character who is otherwise portrayed as villainous and/or hostile to the status quo ("Even Bad Men Love Their Jesus"). Jesus was supposed to be God in mortal form, and as such, having a sense of humor is possible, if not probable. Portraying Jesus as a cool dude can somewhat dent his gravitas as a religious figurehead, and as a result some Christians can get offended by (what they consider to be) the trivialization of their Lord and Savior.
There's also the fact that Jesus is a figure in Islam as well, and general Islamic sentiment is that prophets are sacred and should not be portrayed.
Others may note that Jesus is Way Cool because he happens to agree with the writer on all sorts of subjects, even those where all the evidence is the other way round.
On the other hand, when employed in works that try to play up Christianity as being "cool" by association, it generally gets a free pass.
Always remember that tropes are neither inherently good nor inherently bad, just tools.
The trope is usually associated with atheistic former Christians who are attempting to dissociate themselves from Christianity, but still have issues with it, and therefore need to view/depict Christ as a sympathetic figure, in order to obtain integration, resolution, and catharsis; Kevin Smith's example (from 's attempt to basically include Jesus as a member of their community.
In these cases, it can overlap with God Before Dogma: their issue isn't necessarily with the Lord Himself, just with religious doctrines or practices done in His name.
He also had a pronounced anti-authoritarian streak, regularly calling out religious leaders for acting Holier Than Thou.
Study of the New Testament (and the non-canon Gospels) will tend to show Christ as much less severe than he is sometimes depicted by certain church authorities, who have been known to (ironically) misuse his words with an eye on political and social control.
A character-centric Sub-Trope of Unacceptable Targets. When Jesus surpasses "way cool" and delves into "Freakin' Badass", that's Kung-Fu Jesus.
Compare and contrast Jesus Was Crazy, Hippie Jesus.
When cool people express admiration for him, it's a case of Real Men Love Jesus.