This question is presumably prompted by something someone had read or said about the "Harvard school" mode of interpreting the Aeneid. The Harvard school isn't quite anti-Augustan -- at least, it isn't usually that extreme -- but in some recent discussions it is instead called the "pessimistic" view of the Aeneid's political message.
The Harvard school basically sees the Aeneid as doing the same kind of job as, say, Shostakovich's 5th symphony: as a work of art that, on the surface, celebrates its political masters, but at some less obvious level it contains subversive messages or expresses resent. This isn't quite my area, but I would expect that in some ways the Harvard school was prompted by some less subtle expressions of resentment over the civil war that can be found in Vergil's earlier work, especially the first Eclogue.
For the pessimistic (but not specifically anti-Augustan) readings, there are plenty of gloomy things to focus on in the Aeneid: the symbolism of the golden bough as death, and Aeneas' descent into the Underworld as a journey where only divine aid can offer salvation; Aeneas' explicit death-wish in book 1; Aeneas' endless concessions to fate, about which he is never happy; the fact that when Aeneas leaves the Underworld, he goes via the gate of false dreams; the continual emphasis on grief and tears, often even vain tears (lacrimae volvuntur inanes): Aeneas' emotions are dominated by his sense of loss, more than by anything positive about his destiny. For some readers, things like these are enough to make the surface messages about the golden age to come ring hollow.
The more specifically "anti-Augustan" bits (or, shall we say, "pessimistic about Augustus" bits) are things like the relentlessness and inescapability of violent internecine bloodshed in books 7-12, representing the chaos of the civil war; the continual reminders that authority depends not just on the threat of violence, but on violence itself; and of course the very end of the epic, where Aeneas (Augustus' literary avatar, inasmuch as there is one) ends the war not with clementia but vengefulness and murder, cutting down the helpless Turnus and ending the poem extremely abruptly. This last episode is one of the very few moments in the poem where Aeneas actually exercises any agency: the rest of the time he is usually (maybe even always) a passive agent of the gods or of fate, and does what he's told like a good boy. The one time he acts on his own initiative, it's all about violence and hatred. Aeneas isn't actually Augustus, so it's not quite a criticism, but it's hardly flattering either.
Even within the Harvard school it's too extreme to see the epic as solely anti-Augustan. One seminal 1964 article refers to the poem's depiction of "Roman history as a long Pyrrhic victory of the human spirit": "Virgil values the achievement of Rome... and yet he remains aware of the inevitable suffering and loss". Even if the Aeneid expresses regret at what was lost in the civil war and Augustus' accession, it still recognises the inevitability of Augustus as a necessary part of Roman history.
Edit. There's [a handy bibliographic survey here.](http://www.vroma.org/~bmcmanus/werner_vergil.html#Harvard School) Much as Vergil scholars might wish otherwise, the division between optimistic and pessimistic readings continues to crop up in studies of Vergil and his context, though recent interpretive studies do their best to conceal it by hiding it under more general titles.
It wasn't.
As a matter of fact, it was Augustus who hired Virgil to write the Aeneid, in part as a propaganda tool, in part to embody the national identity and foundation myth.
Now, Virgil wasn't really proud of the Aeneid. Some say it's in part because it didn't turn out the way he wanted it to be, some say because he realized that it would become a tool for Augustus and futher emperors to justify absolute power.
It's said that, falling ill in a travel between Athens and Rome, Virgil asked his friends to destroy the Aeneid draft as his last will. They didn't, of course. Augustus commanded it to be completed without touching the original style, so the editors had to imitate Virgil's style to some extent.
And if there was any anti Augustan suggestion in the draft, I'm sure the editors did their best to remove it.