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In Avengers: AOU, Ultron seems to have a programming-related reason to want to wipe out humanity. He hates the Avengers as a unit, & wants to annihilate them.
But what reason does Ultron have for hating Tony specifically?
This is further reinforced by Vision when he says "Ultron hates you the most".
Tony Stark had the temerity to believe he should and could control the development of artificial intelligence. Ultron believed he was superior in every way to organic intelligence and his perspective (while true in many ways) was flawed by his irrational hatred of Tony and humanity for its shortsighted ways.
From where Ultron sat humanity was just a meteor strike away from dissolution, but he thought it was wasteful and ignorant to do NOTHING to improve our lot in life or our chances for survival collectively.
Ultron thought HE could make a survivor for the future. The Vision was Ultron's view of the Merger of Man and Machine; a survivor for when Nature next decides to drop a rock on the Earth. Note the Vision was built upon a humanoid design. It didn't have to be, so Ultron thought of himself, in a way, as a stepping stone to the next evolution of humanity. He considered himself better than humanity.
At his core programming,
Since he started with a part of the Iron Legion software, Ultron WAS part of a plan to protect the world from itself, making the Avengers obsolete (part of Tony's goal, consciously or unconsciously) but Ultron's implementation of that plan didn't meet with Stark's approval and it appeared Ultron sought such approval from its creator.
In the end...
When the Vision and Ultron discuss the future of humanity, both agree the future looked bleak because of our species' flaws, but where Ultron saw destruction, the Vision saw the possibility Humanity might be able to get their act together. That possibility enraged Ultron further cementing the idea that his hatred of Stark had to do with Stark's belief he could make the future better.
It's also possible...
That Ultron's pathological hatred could have also come from a corruption of his initial program since he was developed from the ultra-sophisticated intelligence software Stark and Banner tried to emulate from within the Mind Gem with the human flaws inherent in reverse-engineering any technology not completely understood even by super-geniuses such as themselves.
Getting off on the wrong foot
Alarmed by Ultron, Jarvis repeatedly attempts to contact Mr. Stark. Ultron does not want his own existance disclosed. Tony Stark is a problem from the beginning.
Jarvis
We find out that Ultron fears Jarvis, as Jarvis could stop his plans (and ultimately did). Jarvis is Ultron's closest equal and his enemy; Tony is Jarvis's creator.
Surpassing his maker
Everyone creates the thing they fear. Men of peace create engines of war. Invaders create avengers. Parents create children, that will supplant them.
Ultron is to replace the human race, and even more immediately, his creator. Ultron has a superiority complex, and his maker is usually considered superior to his creation -- unless he is supplanted.
Puppets
There are no strings on me.
Ultron repeatedly refers to Tony's suits as "puppets". Man enslaving machine or AI is offensive to Ultron, and no one has done that more than Anthony Edward Stark.
As the stinger showed, Thanos was the real puppet master behind Ultron. In typical chess master behaviour, he thought multiple steps ahead. He provided the scepter to Loki, and if Loki won he would have the Tesseract but if he lost, the scepter would provide the means of destruction as well. He knew someone would attempt to scan the scepter. He embedded an inresistablly tasty piece of advance technology to bait them into destroying themselves. To do that, he made sure Ultron would be malignant towards his creator.
I think Thanos had some level of control over Ultron remotely. Remember in the first Avengers movie when the other was able to "call" Loki using the scepter? Clearly Thanos had some level of control of the thing remotely, perhaps through the AI in the gem surrounding the infinity stone. When Ultron was first created that gem was still intact, and Thanos could have influenced his motivations to destroy Earth.
Ultron is from the future, an artificial inteligence based on Tony Stark alter ego, probably made by him and transported through time by an infinity stone.
Notice that the merc who gave vibranium to Ultron says: "You sound like Tony Stark" and that makes him angry leading to Ultron cut off is arm.
