The real answer is that we don't know. There are numerous scholarly interpretations, but none of them can be certain, if only because the available evidence is so limited. Socrates Scholasticus' contemporary account is probably the most useful, but he also had an axe to grind against Cyril of Alexandria, whose struggle against Orestes led to Hypatia's death:

For as she [Hypatia] had frequent interviews with Orestes, it was calumniously reported among the Christian populace, that it was she who prevented Orestes from being reconciled to the bishop. Some of them therefore, hurried away by a fierce and bigoted zeal, whose ringleader was a reader named Peter, waylaid her returning home, and dragging her from her carriage, they took her to the church called Cæsareum, where they completely stripped her, and then murdered her.

The 'Arian' Philostorgius is another contemporary source, but his work now only survives in fragments. The relevant fragment for this event says very little:

Our heretic also says that during the reign of Theodosius the Younger the woman was torn to pieces by those championing the consubstantialist doctrine. She was torn apart by the Alexandrians and her body mocked and scattered throughout the whole city. She suffered this, some say, at the hands of Cyril because of envy of her superb expertise, especially in astronomy.

Note that because this only survives in a later Byzantine work, Philostorgius is naturally referred to as a 'heretic' and his own words were no doubt paraphrased by the Byzantine compiler. In any case, even if this brief account is entirely reliable, it tells us very little about why Hypatia was singled out - aside, of course, from Cyril's envy.

Damascius, a pagan philosopher from the sixth century, is more forthcoming:

Thus it happened one day that Cyril, bishop of the opposition sect [Christianity] was passing by Hypatia's house, and he saw a great crowd of people and horses in front of her door. Some were arriving, some departing, and others standing around. When he asked why there was a crowd there and what all the fuss was about, he was told by her followers that it was the house of Hypatia the philosopher and she was about to greet them.

When Cyril learned this he was so struck with envy that he immediately began plotting her murder and the most heinous form of murder at that. For when Hypatia emerged from her house, in her accustomed manner, a throng of merciless and ferocious men who feared neither divine punishment nor human revenge attacked and cut her down, thus committing an outrageous and disgraceful deed against their fatherland.

However, despite this level of detail, Damascius is a later source and his words were actually written to lionise the philosophers of Athens against Alexandria. Understandably, we should not see in his account a precise recounting of the complex power struggle in Hypatia's Alexandria.

Finally, we have the seventh-century Chronicle of John of Nikiu. According to John, after riots against local Jews, the crowds turned against Hypatia:

And thereafter a multitude of believers in God arose under the guidance of Peter the magistrate—now this Peter was a perfect believer in all respects in Jesus Christ—and they proceeded to seek for the pagan woman who had beguiled the people of the city and the prefect through her enchantments. And when they learnt the place where she was, they proceeded to her and found her seated on a (lofty) chair; and having made her descend they dragged her along till they brought her to the great church, named Caesarion. Now this was in the days of the fast. And they tare off her clothing and dragged her [till they brought her] through the streets of the city till she died.

That's it, these four different sources provide us with all the information we have for Hypatia's death. Interestingly, only Damascius claimed that Cyril directly ordered the attack on Hypatia - in other accounts it was a spontaneous lynching, perhaps organised by someone named Peter (based on John of Nikiu and Socrates Scholasticus). Moreover, the connection with Orestes is not seen unanimously by the sources as the motive behind her murder:

• Socrates - Cyril and Orestes were involved in a dispute and a few hot-headed monks attacked Hypatia, who was closely linked to the governor.
• Philostorgius - Cyril was envious of Hypatia's learning.
• Damascius - Cyril was envious of Hypatia's influence, which may or may not refer to her association with Orestes, but this is not noted by the source itself.
• John of Nikiu - Orestes was too closely associated with Hypatia; when riots broke out, some of Cyril's followers murdered her to end her hold over the city's elite - which presumably referred to her friendship with other high-ranking officials, not just Orestes.

As you will have noted, these sources don't really mention who else Orestes was associated with, so we can't judge whether Hypatia stood out from Orestes' other allies. Edward Watts, who has just published a biography of Hypatia this year, speculates that because she was so socially connected, Orestes had tried to bring Hypatia in to build a coalition of Alexandrians to calm the tensions. This is not as unlikely as it sounds, as Hypatia had Christian students and had evidently survived, even prospered, under the riot-happy tenure of the previous (and equally zealous) bishop of Alexandria. As acknowledged in the sources I quoted, Hypatia certainly seems to be a well-known figure in the city and would have had plenty of contacts for the governor to draw upon to stabilise the situation.

Alan Cameron, another noted scholar, has emphasised another factor, that of Hypatia's gender. Because Hypatia was so connected, perhaps even a celebrity comfortable with both philosophers and imperial bureaucrats, Cameron suggests that Cyril, a newly elevated bishop with a lofty legacy to live up to (his uncle was the previous bishop), was probably indeed quite envious of her position, as described in two of the sources. By being so involved in public life, it also brought to prominence her paganism to the attention of Christians with a different view of a woman's role in society. In any case, Cameron still argues (rightfully, I think) that Cyril could not have actually wanted to murder her, as the bishop was too shrewd of a politician to not realise the harm it would cause. The fact that three out of the four sources condemned her murderers (apart from John of Nikiu) certainly suggests that contemporaries in the fifth century were similarly aghast at Hypatia's death. It is unfortunate then that it is impossible for us to recover the mob's motivations.

Personally, I would also add that while Hypatia looms large in the sources because she was important at the time, surely her fame also grew with each telling of her murder, so much so that the majority of the people involved were forgotten by history. For example, we know from Socrates and John of Nikiu that Cyril had tried to turn Ammonius, one of his followers who had died in the riots, into a martyr-figure. Had Cyril comprehensively won this power struggle, it would not be too far-fetched to suggest that we would now speak of the pious Ammonius, who was tortured to death by the tyrannical governor of Alexandria. But who remembers him now? As the earliest sources noted Hypatia's death because she was already a celebrity, she is now the only person we can name who was linked to Orestes' struggle against Cyril - even if in reality it would have been much, much more complicated!

For further reading, E. Watts' Hypatia: The Life and Legend of an Ancient Philosopher (2017) is excellent and his previous work, especially City and School in Late Antique Athens and Alexandria (2006), provides additional context for Hypatia's life and times. Alan Cameron's recent essay on Hypatia can be found in his Wandering Poets and Other Essays on Late Greek Literature and Philosophy (2015), which is meant for a scholarly audience and so is more expensive, unfortunately.