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According to Star Trek (2009) movie, Kirk became captain of USS Enterprise NCC-1701 when he was much younger than he was in TOS. In TOS, it was shown that Christopher Pike was captain of Enterprise 13 years prior to Kirk's 5 year mission. Why was Kirk replaced with Christopher Pike?

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J. J. Abrams has confirmed 100% that the 2009 film is in an alternate timeline to TOS, so the events for Kirk and Pike can be completely different between the two.

The notion that when this one character arrived – Nero – that basically the timeline is altered at that moment. So everything forward is essentially an alternative timeline. That is not to say that everything that happened in the original series doesn’t exist. ... We are simply saying that from this moment in the opening scene of the movie, that everything people knew of Star Trek splits off into another timeline.

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    In-universe: TOS has displayed planet Vulcan. It means, TOS was indeed from old timeline. I forgot about that.. – Captain Cold Aug 10 '12 at 9:56
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They're not in the same continuity. The 2009 film exists in an alternate timeline to TOS.

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    @SachinShekhar: Spock explicitly describes it as an alternate timeline in the move. – Keith Thompson Aug 10 '12 at 8:30
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    @SachinShekhar have you actually seen the film? The whole thing is about the creation of an alternative timeline. – Daniel Roseman Aug 10 '12 at 8:43
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    @SachinShekhar BECAUSE THAT'S THE WHOLE POINT OF THE FILM! Nero goes back in time in order to destroy Vulkan as revenge on (original) Spock. As a result, all sorts of things happen that didn't happen in the original timeline, like Kirk's father being killed. And original Spock is actually there in the new timeline to explain the differences! I absolutely don't understand how you can claim it's not a new timeline when it is absolutely 100% explicit that it is. – Daniel Roseman Aug 10 '12 at 9:07
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    Similar events within the actual TOS may occur later in this new alternate reality, but the simple fact that the changed histories and origins of these characters means that it is not the SAME timeline. Just because Kirk and the crew go to the same planet or meet the same person in two separate realities does NOT mean that they are the same timeline - even if it is on the same dates. – phantom42 Aug 10 '12 at 12:45
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    @SachinShekhar: In the TOS episode "Amok Time", the Enterprise visits Vulcan, which no longer exists in the alternate timeline. In "Journey to Babel", we meet Spock's mother Amanda, who died on Vulcan in the alternate timeline. In "Balance of Terror", Kirk and Spock were astonished when they saw what Romulans look like; in the alternate timeline, they've already met Romulans. – Keith Thompson Aug 10 '12 at 17:35
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In the original timeline, Kirk succeeded Pike as captain of the Enterprise. Pike was promoted and later badly injured, as seen in the TOS episode "The Menagerie".

In the new alternate timeline:

Pike was still captain of the Enterprise, but events unfolded differently. Certain things happen similarly to the way they happened in the original timeline, but several years earlier and with significant differences. Pike is injured at the hands of the Romulans rather than by exposure to delta rays. We see him in a wheelchair at the end of the movie; presumably he is unfit to continue as captain, or at least unwilling to do so. Meanwhile, Kirk has demonstrated an outstanding ability to command a starship (again, several years earlier), and is given command of the Enterprise. In the original timeline, he didn't have the opportunity to demonstrate his ability this early, and Pike remained in command of the Enterprise so it wouldn't have been available anyway.

The numerous parallels between the original and alternate timelines require, IMHO, considerable suspension of disbelief. The members of the crew follow very different paths in the two timelines, but both sets of path lead to the same end, with all of them serving together on the Enterprise. Either it's a case of artistic license (which I'm willing to accept), or there's some explanation for the parallels that might be explained in future movies and/or books.

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In TOS, Kirk got the Enterprise, when both he and Captain Pike got promoted. Pike got crippled in an accident aboard an unnamed starship.

In the Abrams film, Pike was captured and crippled by Nero, which led to Kirk taking command, and Kirk's official promotion.

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