The Borg Collective are unambiguously villainous antagonists - they carry out the theft of whole civilizations and the kidnapping of trillions of people on a galactic scale, killing billions who get in their way. They're mass enslavers and technological rapists who violently absorb cultures enmasse, so they're bad guys through and through.
However what is reactionary about the demonization of the Borg is that they're cyborgs and they're a collective, which is not bad in of itself depending on the context. There was nothing wrong with the Mongolians being nomad horsemen, but it was their war crimes and aggressive conquest of Eurasia that had earned them their infamy. The way our technology has progressed since the airing of "Q Who?" points our civilization more towards the Borg Collective instead of the United Federation of Planets, with our Internet being a primitive form of the Borg Collective.
If we meet people from the future when we're a space faring society they're going to be like Data and Seven of Nine, instead of O'Brien and Scotty. If we're going to be deep in space for years/decades/centuries at a time, our warm and fleshy bodies are going to be a detriment, and nano machines will be useful in repairing our ships and our bodies. Brain implants make communications to computer nodes and each other more efficient.