I had read a few years back that using a VPN to anonymize your IP was a flag that could cause you to be a target for government hacking attempts. Look, I am not arguing the government does shady shit, but this article and this judge's words as they are being used, are bullshit. And I'll bet in both cases that you sited (first, let's go ahead and accept that we live in a police state at this point in time, because if you don't expect that you're fucking naive as hell) there was a motive at the base of the investigations that included doing shit that a normal person would likely be glad if the targets of the investigation were caught.

So sure, the government and police agencies are sifting through innocent people's data, and it is slimy as fuck, and likely often illegal. But what this judge is saying is that if you are on the internet and expect to have privacy, regardless of what tools you're using, you are being naive. And he is right. He is not saying if you are on the internet that means the FBI is allowed to look at data on your computer. As far as the law goes, there is criteria that still needs to be met to do that, though likely it is being done, often, without said criteria being met.