My own theory about about why Gregtech spawns such ire is based upon one key observation. The quality of Gregtech is inconsistent.
There are hundreds of minecraft mods that people have just turned out for practice, to prove that they can, or to implement some poorly thought out feature that "sounds cool". The negative qualities of these mods are far worse than things like gregtech, yet even on their own respective forum threads, nobody really gives a damn about them. If Gregtech was universally terrible, it would be removed from peoples' modpacks without a second thought, and there would be very little to say about it.
Except its not universally terrible. It actually has a lot of interesting features. The fusion reactors are cool, the whole chemistry aspect creates a slew of interesting systems to set up, and there is a lot of depth in setting up the multiblock machines. On the other hand, resource processing (even with automation) does frequently turn into something of a grind, the documentation is categorically terrible, and the changes to other mods can alienate people who just want to experience the mod in question, without having to delve too deeply into gregtech. Couple this with the fact that Greg seems to not even want to engage in discussion with these issues (let alone consider if there is a way to correct them without disappointing the core fanbase), then we have a recipe for really pissed off players. Other mods tend to be more polished, and less schizophrenic with what they are trying to achieve, thus, if people don't like them, they can leave them be without feeling as though they are missing something cool. However, the fact that gregtech does have some cool things means that many people are frustrated. They want the cool fusion reactors and chemistry sets, without the grind and molestation of other tech trees.
Invest a little ego in this, and you have a recipe for conflict. Many of those who play gregtech to get the cool stuff are forced to justify the naff bits when they talk with other people. Likewise, many of those who dislike the grind need to put down the cool bits in order to justify their choice of not playing gregtech. Such is the way of the internet.