It's very difficult to say with any degree of conviction who was right and who was wrong in this particular struggle, not least because it was primarily sparked by personal animosity rather than a clash of principles.
Bacon was certainly justified in feeling aggrieved at the threat that the Virginian Governor Sir William Berkeley's new policy posed to his livelihood. At the same time, Bacon was a notorious troublemaker, who'd originally been sent to Virginia by his father in the hope that he would mature. So one gets the impression that Bacon would've rebelled against the authority of Sir William—his cousin by marriage—sooner or later.
On the whole, one would have to say that Sir William emerges as the more sympathetic character of the two. He showed a genuine concern with maintaining amicable relations between the English settlers and the Native American tribes. That's why he implemented the restrictions on trade with local Indian tribes that caused such anger among Bacon and his followers, who felt that they were being deprived of their livelihoods in favor of Berkeley's cronies.
One could argue that Berkeley's policy, for all its evident flaws, did nonetheless represent an honest attempt at reducing tensions between the English settlers and Native Americans. Bacon wasn't interested in any such accommodation. He simply wanted to exploit the local tribes for all they were worth while maintaining a hostile stance towards them. Bacon's rashness and impetuosity stand in stark contrast to the statesmanlike demeanor of Sir William Berkeley, who generally showed real leadership qualities throughout the whole sorry business.
While there's no doubt that Bacon and his followers had perfectly legitimate grievances, the way they sought to remedy them was excessive, to say the least. Behaving like an out of control mob, they frittered away what sympathy they had by engaging in acts of killing and wanton destruction. In doing so, they undermined their own cause as well as the stability of Virginian government and society.
There are a few things that you might consider when determining if a revolt was justified. First of all, it is important to look at both sides unbiased. Was one group being marginalized or treated unfairly? You might also look at society as a whole. For a revolt to be justified, it should be focused on achieving more equality for all.
If we look at the two sides in this conflict, we will see that it is actually quite personal and seems to be focused on the Baconites merely showing unrest about the social, economic, and political environment in Virginia. Unlike a justified revolt, they didn't really seem to be fighting for anything in particular, other than trying to take down the government in Virginia. In fact, it is now recognized that Bacon's Rebellion was not related to the origin of the American Revolution. Additionally, if we look at the history of Bacon, it appears that he was known for being a troublemaker, and, as a cousin of Berkeley, this might have more likely been a personal conflict.
The question of justification is always a difficult one to answer, particularly when it comes to the question of revolution. Ultimately, the question becomes whether Bacon’s motivations justified his actions, and whether the Baconites were justified in addressing the perceived threat of the Native American tribes in the way they did. Like Berkeley, Bacon seemed to be acting not merely on the idea that the lives and livelihoods of colonists were at stake. Berkeley benefited a great deal from trade with the Native Americans, and Nathaniel Bacon, also seeking to improve his own lot, tried to get in on the trade; however, Berkeley and a number of his close associates snubbed him in his bid for power. Based purely on this perceived insult, perhaps the Baconites were justified in their rebellion. Concerning Bacon’s other actions during the rebellion -- particularly the pursuit of the governor and the burning of the capital at Jamestown after the governor declared Bacon a rebel – his actions were certainly not justified.
When looked at from another angle, however, the picture appears quite different. Bacon, in his zeal, did not bother to specify or distinguish between different Native American populations, assuming them all to be more or less the same. Bacon took as his primary target the Susquehannock Indians, a tribe that was quite peaceful and posed no serious danger. Whether the threat was real or only perceived, the fact that Bacon and his followers showed no real concern for the objects of their pursuit suggests they were not justified in their actions.