In the future, much of the population has chosen to live inside a virtual utopia, but when a routine upgrade goes awry and creates an AI hell bent on wiping the system clean of humanity, a plucky young programme must choose between his people or face deletion with his adoptive human family.

You are using too many words to describe a plot. Regardless the complexity of the setting and the difference to our “normal” world the plot is what should dominate a logline and currently this draft reads more like a watered down description of an intricate world.

Take Avatar as an example, like the movie or not, Avatar was one of the most successful movies of all times and was set in an equally complex world with many intricate details. However the logline for Avatar focus on Jake’s plot not the world, setting or background.

In this instance you could do away with many of the descriptions and cut to the chase, figuratively and literally, and start with the inciting incident:

After a rouge AI threatens to wipe out humanity in a virtual Earth of the future…

I would be weary of scifi stories that priorities VFX over story. Nothing in this logline is particularly original and would likely not impress most executives or producers. It is very hard to do so with heavy VFX and grand setting movies now days but it would be far more likely that a producer or executive would be impressed with a good story.

As it stands the main character is a young program, can a program have an age? Or is it a program of a young boy? Best to depict the MC as humanly as possible.

What does “…choose between his people or face deletion with his adoptive human family?” mean?
This statement is creating confusion not intrigue.

Are these flesh and blood humans or humans that uploaded their consciousness to the virtual grid? Is the MC a person to have his own people or is he a program? In this future virtual world there is an adoption plan for programs why? Can there be orphan programs? In a virtual world anyone can reprogram themselves to be able to bare children why need to adopt? Why does humanity choose to live in a virtual world? How could most of humanity unanimously agree on such a drastic move?

Make the stakes clearer and the details plausible yet include only information vital to understanding the plot not the setting. There are too many questions raised by this logline that distract from understanding the plot at hand and place the suspension of disbelief in doubt at this early stage.

Lastly this logline describes a weak plot because there is no clear goal for the MC to achieve. The logline ends on a dilemma not action: “…choose between his people or face deletion?”. What could make this an interesting story to watch is the action he does after making his choice as appose to making the choice.

Hope this helps.