According to director McG:
"Kyle Reese must be kept alive, so he can be sent back in time from 2029 to protect Sarah Connor, impregnate her, and she'll give birth to John Connor, who will save us all. And the simplest way to understand that is to protect the triangle of Kyle, John and Sarah. Any deconstruction of that leads to more headache than satisfaction." (TerminatorChronicles.com)
In other words: Skynet already knows Kyle will travel back in time and become John's father. It also knows that in the near future, as a desperate measure, it will try to alter the past in its own favour. In 2018, Skynet may not be ready yet to change the time-line, thinking it can still win the traditional way. The effects of altering the past are impossible to predict: with Connor removed from the time-line, perhaps someone else will grow up to be the leader of human resistance, who could be even better than Connor (Skynet obviously didn't consider this when it sent the Terminators back to eliminate him, or maybe it just didn't care at that point given that John & Co. had breached its inner defenses and it was about to be destroyed.). Best strategy for Skynet to win in 2018 is to lure Connor when he is rising to power, kill him then, and leave the resistence in disarray.
Another theory, Skynet probably didn't want to cause a time paradox, if he killed Kyle the future of 2018 would be reset, the future would cease to exist, and Skynet would have to start all over again and may even destroy itself in the process.
The reason why Skynet tried to destroy Connor before he was born in T1 was because Connor destroyed Skynet in the future like Kyle said "Skynet's defense grid was smashed, we'd won, taking out Connor then wouldn't have made a difference, Skynet would have to eliminate Connor's total existence."
But Connor didn't destroy Skynet yet so it thought it would be easier to use Kyle as bait and kill Connor now before Connor destroyed it. With Connor dead and Kyle still alive, Kyle would still go back in time, Connor would still be born and Skynet would win the war.
In other words, it would be easier to kill Connor now and Skynet would win the war in 2018 instead of killing Kyle, reset the future, and start all over again.
Another theory is that three different theories of time travel are used. In Terminator 1, they introduced the idea that time is static, like a train track. Everything that happened was meant to happen, and the outcome would be the same no matter what the characters did. The second film introduced the idea of alternate realities. In this reality, Skynet was destroyed and then the characters could pick and choose their own futures, and the future of Kyle Reese would never exist. The third film used the idea that time is fluid, like a river. The events of the 2nd film changed history, but couldn't rewrite it. Future events would still happen; they could be delayed, but never eliminated. The fourth film tries to go back to the idea of alternate realities, in that this future is different than Kyle Reese's original future, but it appears that there were so many plot holes, they're actually back to using the "time is fluid" idea.