I think the article is wrong about this. The linked EFF post mentions nothing about passports and the TSA currently accepts a wide range of ID documents for domestic flights:
Which makes sense because if you're opting out of the new automated process then you just go back to the manual process - somebody looking at your documents. Those document requirements have not changed.
In 2020 when REAL ID comes into effect then you'll need a special ID (typically a new drivers license), or failing that, a passport - but that's a separate issue.
https://www.tsa.gov/travel/security-screening/identification
Which makes sense because if you're opting out of the new automated process then you just go back to the manual process - somebody looking at your documents. Those document requirements have not changed.
In 2020 when REAL ID comes into effect then you'll need a special ID (typically a new drivers license), or failing that, a passport - but that's a separate issue.