This is an awesome topic. Thank you both for your response! I try to convert everything into programming terms to make it a bit easier to understand, but it's a really complex topic imo.
Thanks for your comment. I quickly searched for the IM protocols and there are plenty of open-source projects with promising functionalities.
I think that the mindset of the majority of the people is the source of this problem. Most of the people I speak to don't care about their privacy. They say that they have nothing to hide and that's a valid statement. The problem is that we don't get to choose. If someone wants to share all of their personal information it's their choice, but to not share your personal information seems almost impossible. Social standards expect that you have WhatsApp and LinkedIn and such.
I'm facing the same problems. All the people in my (real life) social circle are using WhatsApp. All of my friends are calling me crazy that I don't have Instagram, so talking about alternative messaging apps is probably not going to work. I think this is true for most people in the western culture. I value my privacy, but the struggle is to big for me.
Maybe an open-source protocol, like how e-mail works, could be a solution for this problem. That you can choose your messaging apps and that they can interfere with each other, like email clients.
Another wild thought: Is it possible that the solution for harmful retroviruses, like HIV, are retroviruses itself? If retroviruses can overwrite or fuse with our DNA, can't we overwrite it back by making a retrovirus ourselves?
I'm not familiar with this topic at all, but it's super interesting.