In the late ’90s the Dalai Lama banned the practice of the Dharma Protector Dorje Shugden, and his followers began to enforce this ban within the Tibetan community causing disharmony and immense suffering. Since this practice is one of the key practices of the New Kadampa Tradition (NKT), and to support fellow Tibetan Dorje Shugden practitioners, NKT practitioners joined in protests against the Dalai Lama’s ban. They were not wrong in protesting against the Dalai Lama’s suppression of the right and freedom to engage in this traditional religious practice. For the reasons why Kadampa practitioners everywhere oppose the Dalai Lama’s ban of their Protector practice, please see Wisdom Buddha Dorje Shugden.
However, it was the International Shugden Community (ISC) that organized protests against the Dalai Lama’s ban, and not the NKT. The ISC was an ad hoc coalition of Dorje Shugden practitioners — including NKT practitioners — from many different countries, and included more Tibetans than Westerners.
Some NKT detractors created websites and blogs to allege that it was the NKT that was organizing demonstrations against the Dalai Lama because there were many NKT practitioners visible at the demonstrations. However, people who attended the demonstrations did so as individual Dorje Shugden practitioners, not as representatives of the NKT. Most people who practice Gelug or Kadampa Buddhism rely upon Dorje Shugden as their enlightened Dharma Protector, so it is not surprising that there were a great number of Kadampas supporting the protests. See also What is the relationship between the New Kadampa Tradition and the International Shugden Community?