Here are some numbers, FWIW, might be of no value at all, you decide.
First look at
FAA Pilot Data, and run the percentages. Here is what my spreadsheet showed:
Percentage of FAA certificated pilots that are female by category:
All pilots: 6%
Student: 12%
Recreational: 6%
Sport: 3%
Private: 7%
commercial: 7%
ATP: 4%
So, what does this tell us? Let's add one more:
ALPA members: 5%
There are a total of 53,000 members of ALPA.
There are 5,636 female pilots with ATPs.
There are 8,289 female pilots with commercial certificates.
Unknown are if the commercial certificates might have ATPs for multi engine. It is clear that ALPA has 2,650 female pilots according to the CNN article stats. Of course, there are many airlines that are not part of ALPA, so the total numbers of female airline pilots is actually higher. There are a total of about 79,000 airline pilots in the U.S. Assuming the 5% holds (which is most likely), that means we have almost 4,000 female pilots in the airline industry, and about 75,000 males. Now compare:
There are about 139,000 male ATPs.
There are 5,636 female ATPs.
There are about 125,738 males with commercial pilot certificates.
There are about 8,289 females with commercial pilot certificates.
Is it safe to assume that most airline pilots hold an ATP? If not, would that percentage be different by gender? I do not know. If we assume for simplicity that they all have ATPs, then it appears that roughly half of all male ATPs are employed by airlines and roughly 70% of female pilots are. What is the ratio for corporate? What percentage of those male ATPs are corporate pilots vs. female? If there is a larger disparity there, that might explain the difference. I have no idea.
It appears that more men seem to want to fly airplanes for fun based on the rec certificates. The percentages for captain's is lower, but as the system is entirely seniority based, in my experience that is more due to women choosing seniority over seat position (QOL vs. pay/prestige). Nothing wrong with that, and it makes sense.
The larger issue is that not that many women seem to want to be pilots. Typical for my wife when she tells someone I'm a pilot, the men say "I always wanted to do that", the women make remarks about "aren't you worried about him", or other remarks that are not about how they would like to do it. There are a lot of factors into what people choose to do, and I am not sure that we will be able to change that.