Kufa (الْكُوفَة al-Kūfah) is a city in Iraq, about 170 kilometres (110 mi) south of Baghdad, and 10 kilometres (6.2 mi) northeast of Najaf. It is located on the banks of the Euphrates River.
I have not seen any one who claims that Imam Ali's house water is bitter. Nevertheless, even if some claims that, it does not harm the sacred status of the place. The location of the house is near the river of Furat. Sometimes the water level in the river is high and sometimes it is low or even very low. That can be a possible reason of change in the taste of the water. It is worth mentioning that the house was never owned by Imam Ali (AS) but by his nephew (Jo'dah ibn Hubairah جعدة بن هبيرة)and Imam Ali (AS) was just a temporary tenant in that house.
Thank you for your question. There was a group of people that were enemies of the Imams (as) in Kufa but generally speaking Kufa has been a stronghold of the Shia and that is why Imam Ali (as) chose it as his capital. There were Shia in Kufa that joined Imam Husayn (as) and others that were prevented through imprisonment. The hadith of Ahl al-Bayt (as) were also wide spread in Kufa during the lives of the later Imams and the Shii Kufan population was subject to oppression many times during the reigns of the various caliphs. So the premise for the question is not accurate as it is one sided.
May you always be successful.