simple enough

Pike was captain for the Pilot episode
while the ABC Exec's did'nt like the Pilot, the commissioned a second Pilot with Shatner as Jim Kirk.
that one they liked...
the Original Pilot was then used in bits for a later episode.

"The first officially known commanding officer of the Enterprise was Christopher Pike, who served as captain for more than a decade prior to Kirk's fabled voyages. Star Trek: The Animated Series revealed a previous captain, Robert April, however as TAS was not considered canon by Gene Roddenberry or Paramount Pictures, owners of the Trek franchise, April's tenure as captain remains a matter of fanon, not canon, until a future live-action film or TV series establishes otherwise. (It has been reported that April is identified as the first captain of the NCC-1701 on a computer display visible in the Star Trek: Enterprise episode "In a Mirror, Darkly", however this has not been verified.)

The second captain of the Enterprise was Captain Christopher Pike which was chronicled in the original pilot episode "The Cage" and the later episode "The Menagerie". A Vulcan science officer, Mr. Spock, came to serve on the Enterprise under Captain Pike's command.

The third captain of this ship was Captain James Tiberius Kirk."

Wikipedia - http://en.wikipedia.org/wiki/USS_Enterprise_(NCC-1701)