Terribly, at least by Romans--we don't really know what the Egyptians thought (and it's also difficult to figure out what the different social elements within Egyptian society would've thought). But we know that the Romans despised Antony's relationship with Cleopatra, because there's an enormous body of work on it in our textual corpus. However, why is this? Why was Antony's marriage to Cleopatra demonized but Caesar's affair with her escaped notice, despite the fact that Caesar went so far as to actually bring her to Rome with him? The answer, as with most things Cleopatra-related, lies with Octavian. Our idea of Cleopatra is so intensely colored by what Octavian wanted people to believe about her that nearly everything that is said about Cleopatra by historians is pretty much assumed to be garbage, but unfortunately we don't have any other evidence.
Octavian's civil war against Antony was the climactic event of a long series of wars that Octavian and Antony started, which devastated Italy and really messed Roman society up. While Caesar's wars had been relatively mild, in that they bypassed Italy and didn't involve any proscriptions or mass slaughters of Roman citizens, Octavian's early career was not quite so spotless. While in later years he would profess to despise the sort of bloodlust that Gaius Marius and Sulla allowed their followers to become prey to, the truth of the matter is that Octavian wasn't a very nice guy when he first appeared. Octavian wrestled control of the Caesarians from Antony basically by borrowing money to raise what was essentially a gang of armed bodyguards loyal to the name of Caesar, and then by stealing legions away from Antony, despite the fact that he had no official magistracy and could not legally control armies. He then duped the senate into awarding him an extraordinary magistracy to chase down Antony and finish off the remaining Caesarians, devastating Italy in his march north to the Alps, and ended up joining Antony instead. And while the war of Philippi was relatively safe for Italy (despite the fact that Antony and Octavian killed the last remaining Republicans they had still kept massive battle from Italian soil) they came back and instituted the largest wave of proscriptions in Roman history, butchering thousands of citizens (which was, apparently, Octavian's idea). And then while Antony went off to the east Octavian started up the War of Perusia, the War of Brundisium, and the war against Sextus Pompey. In all of these struggles Italy and the Italian people--Roman citizens who had been spared massive bloodshed since Sulla had left--bore the brunt of the fighting. As a result of this and the extremely controversial way in which he had gained power (more on this in a moment) the elder Augustus spent a huge amount of time trying to legitimize his rule in his later reign. In particular, he had gained power basically through military means, even more than Caesar. Caesar's opponents had declared his actions illegal and wanted to prosecute him (which was in itself probably an illegal action) but Octavian had gained power by snatching the Caesarians and their armies from Antony, forcing the senate to give him an extraordinary magistracy, stabbing the senate in the back, and massacring his opponents. Finally, the special privileges which Augustus held as emperor derived from certain privileges that Octavian had wrestled from the senate before going off to fight Antony in the war of Actium. These included tribunate sacrosanctity, as well as the office of pontifex maximus, extraordinary magisterial powers (which included, of course, imperium), and the personal oath of loyalty of every Roman citizen. Now these are all powers which the senate is not going to grant to just anyone. Extraordinary magistrates were fairly common, but to give one (and mind you, he was also consul at the time) tribunate powers basically means that Octavian could veto any legislation, tell anyone in the senate to sit down and shut up, prosecute anyone, and was exempt from all kinds of prosecution and legislation. The way he got all these powers was by convincing people he needed them--remember that after Philippi the only people left in the senate were people who Antony and Octavian had put there, so it was mainly a matter of either bullying Antony's supporters into submitting or convincing them Octavian was right--or by force. The former was how he got tribunate powers, by convincing the senate that he needed them to restore the order of Italy, which was currently in a state closely approaching anarchy. The latter was how he got every city in Italy, every Roman citizen, and the entire senate to swear loyalty not to Rome, the people, or the senate, but to Octavian personally--he surrounded the curia with his praetorians and ordered the senate to swear loyalty. Dude needed some good PR after all that, so he was very willing to go out of his way to legitimize himself.
Ok all that's fine and dandy, what does it have to do with Antony and Cleopatra? The thing about Octavian's war with Antony is that had Octavian just gone off to fight Antony just to get rid of him, that wouldn't have gone over too well. Antony was a Roman citizen--a triumvir, no less--and to provoke civil war against a guy that a lot of people still stood behind and whom Octavian had been formally allied with (as opposed to Caesar and Pompey, whose illegal deal was something more along the lines of an under-the-table-agreement) was not really something that very many people wanted, particularly when Italy was in such a shambles and the most important thing was to rebuild. So Octavian needed to justify war against Antony. He did this by demonizing him. It's very clever how this was done, actually. Octavian first spent several years building support for the idea that Cleopatra was some foreign seductress with her talons so far in Antony that he had no idea what was going on. Octavian painted an image of Cleopatra as the sinister eastern queen, using Roman citizens--one of the most distinguished Roman citizens--as tools to rebuild her family's empire and undermine Roman power. Now, whether this was true is a totally different matter--Octavian got people to believe it was true. But what really turned Roman opinion against Antony wasn't even something that Octavian did. Antony fucked up when he formally announced the Alexandrian donations, which granted huge swathes of Roman territory to Cleopatra and her children. This, combined with the fact that Antony had turned his wife Octavia, Octavian's sister, away (his marriage with Cleopatra would not be announced until later, although it's probable that it had already secretly occurred) was intolerable. The Roman people, egged on by Octavian, saw this as a betrayal of the Roman state and an insult to the Roman people. The announcement of Antony's wedding to Cleopatra and the (illegal) reading of his will by Octavian, in which it was revealed that he was basically leaving everything he had to Cleopatra and her children, was the last straw. At this point Octavian had the Roman people sold, and promptly declared war on the dynasts. Even now, though, Cleopatra was a much easier target than Antony, who, for all his mistakes, was still a Roman citizen. So it was Cleopatra's armies and fleets which Octavian told the Roman people would be swarming all over the shores of Italy, and Cleopatra who planned to make herself queen of the Romans, not Antony who, of course, was the one doing all the real work. Octavian used Cleopatra to manipulate Roman sensibilities, to turn what was in the end a rather squalid war fought for pretty petty reasons (Antony really wasn't bothering Octavian over in the east, Octavian just wanted it all and he wanted nobody to be in a position to challenge him) into a noble crusade in defense of Italy against the foreign menace.
Not everyone bought this, of course. But even those who did had to be very careful when talking about Cleopatra. Sympathy for Antony appears quite often in Augustan literature, sometimes quite prominently. But sympathy for Cleopatra is almost always veiled. Take Horace I.37, for example. The first part of the poem trashes Cleopatra ruthlessly, calling her things like the "fatale monstrum" and other really nasty insults. But the second part flips that on its head, emphasizing Cleopatra's nobility in defeat and how she met her fate with head held high. After all those nasty things that's what Horace has to say about her? Whether we buy the idea that Horace had ambivalent feelings about Cleopatra or even felt suppressed support for her (Horace had, after all, been with the Republicans at Philippi, and though he always appreciated Augustus' sparing of him and Maecenas' decision to bring him to literary prominence, he had mixed feelings about the loss of liberty) it's clear that at the very least he wishes to remind people that Cleopatra was a human being, amidst all the rhetoric Octavian was spewing about how she was some sort of eastern demon. And there have been many attempts to connect Cleopatra with figures in the Aeneid. I don't know how much I buy the idea that she's Dido and that Aeneas' decision to abandon her is a reinforcement of Augustus' own sacrifice of personal gratification for his duty of leading the Roman people, but I find the idea interesting, considering how sympathetically Virgil presents Dido. And Camilla has been compared to Cleopatra, which I have somewhat more support for (although a lot of people say a lot of things about Camilla). Virgil has this strange grudging appreciation and respect for Camilla, even though she's a menace, and it's certainly compelling to read her as one of Virgil's many veiled jabs at Augustus (as is, I suppose, the idea that he stabbed Cleopatra in the back, if we accept Dido as Cleopatra).