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In the Matrix, Neo is picked up by the Agents almost immediately after his encounter with Trinity and during his call with Morpheus.
My question is, why didn't the Agents just pick Mr. Anderson off before he became Neo (the Agent conquering bad-ass)
Did Morpeus/Trinity's contact with Mr. Anderson trigger his location off on the radar of the Agents?
The Agents didn't care about Neo at all. They had no idea he was going to become the big Hero, probably because they've never been to the movies and didn't know who Keanu Reeves was.
The agents only wanted to find Morpheus so they could get the access codes to the Zion mainframe. They knew Morpheus was looking for Neo so they hoped to recruit the new kid to help Cipher betray the other free humans.
Up to that point Neo was being tracked by the agents. So presumably it was in their interests to let him interact with Morpeus and Trinity.
If The Matrix was taken as a stand-alone film then it seems like a plot hole, why not be cautious and kill humans who appear to be a risk? However, more is discovered about "The One" when Neo meets the Architect in The Matrix Reloaded
Spoiler:
The One's purpose is to return to the Source, resetting the Matrix to its prime program. Afterwards, he will choose sixteen females and seven males to repopulate Zion and provide another round of humans for the "rebellion".
Your question is answered in the movie by Morpheous. After he wakes up in his house, Morpheus calls him and says to him "If they knew what I know, you would probably be dead."
In the third comment, it is mentioned that it is strange why they don't kill a threat. At first I think they don't want to kill a person that may lead them to the Legendary Morpheus (as Angus said in the first comment) and secondly they don't want to kill a battery!
