Methinks the argument is that STEM distribution should be commensurate to the population make up. So when using your pop. stats, they're still underrepresented.
Using the numbers from Pew 17.3 million people are in STEM. This would put Black participation at ~1.6M and Hispanic participation at ~1.2M.
According to the census 328,239,523 are in the US.
This gives us approximately 42.7M Black people and ~59.0M Hispanic people.
Let's devise a new measure. Population Adjusted Representation. This number is defined to be [Population in STEM] / [Population of US].
So their population adjusted representation is 4% for Black people and 2% for Hispanic people.
Comparing this to White participation:
There 60.4% of the US is White. Around 198M people. According to the article 69% of the field is White. Though this is slightly disingenuous because "White" is a far less clear definition of race than "Hispanic" or "Black". "Asian" is also ambiguous - did they include Indians?
Anyway, 69% of 17.3M gives us around 11.9M people.
So for Whites, the population adjusted representation is 6%.
Summarizing: Whites have a 6% PAR, Blacks have a 4% PAR, and Hispanics have a 2% PAR.
We could make an argument that Hispanics are marginally under-represented according to PAR but Blacks and Whites have a nearly fair PAR.
If you really wanted to make a fuss that 2% gap could be fixed but 2% is not nearly as bad as this article playing chicken little makes it out to be.