You’re mixing up a number of distinct concepts and problems. The ACLU’s advice is not meant to insulate you from lawful investigatory procedure. It’s meant to help minimize the likelihood that you will be convicted of a crime and to maximize the likelihood that unlawfully-obtained evidence will be suppressed at trial.
They say in the U.S., “you can beat the rap, but you can’t beat the ride.” This is true. You can assert your rights, but it’s best not to interfere or say anything other than “I do not assent to search” during the initial encounter. But you might be arrested, taken to jail, etc. Does it suck? Yes. But if I have no other choice, I’d rather spend a week in local lockup while everything gets cleared up than a year or more in state prison (and potentially the loss of other rights afterwards) because I got convicted of a crime.
Sometimes there is just no way out of a bad police encounter here. I wish there was, but the best we can do as a society is vote to change the laws around policing.
Finally, keep in mind that your perspective may be distorted by the news, in a sort of reverse survivorship bias. For every instance of police abuse during an encounter, there could be 10 or 100 where asserting one’s rights leads to no dramatic episode at all, and where the ACLU’s advice led to a conflict-free outcome. You don’t have the full picture, and it’s best not to draw conclusions with certainty if you’re not an expert. (Even experts usually temper their analyses.)