As an atheist, I would say that the opinions of these organisations do matter, insofar as they are likely to influence political opinion in the countries where they have significant followers.

Separation of church and state matters

It matters to people who live in Muslim-majority countries.

poor bastards

Isn't it better to actually consider their arguments than dismissing them for being just who they are? Many of these people are extremely skilled in philosophy and ethics

Although their arguments often are based on religious grounds that you may dismiss, you may also find that similar principles can be derived from humanistic traditions alone.

They get dismissed because they are toxic people and there is no value in dealing with them. They kill kids and entrap people and break them so they can keep exploiting people. Its a system of exploitation. If you're under 8yo, you can believe in Santa, but once you're old enough, you shouldn't believe in imaginary friends that someone else made up, especially if those imaginary friends are psychopaths.