Usually when this is called a problem it is done along with making the implicit or explicit suggestion that men in scientific fields are sexist and somehow discriminate against women. But I, like most men in science, would severely reprimand anyone who treats women unfairly. Therefore I find it extremely unwarranted and unfair that feminists think it is OK to accuse us of sexism without evidence. And I find it saddening that not more men have the courage to speak up against these accusations.
I'm sure there have been cases of discrimination against women in science, but this in no way proves that it's widespread, or that it's affecting the number of women in science.
[* The logic goes that since men and women are identical, there should be just as many women in science as there are men. But this conclusion is unwarranted because the premise is unsupported by evidence.]
If you change the gender of a name and leave everything else constant on an academic CV, acceptance rates go down from 70% to 45%. http://dimer.tamu.edu/simplog/archive.php?blogid=3&pid=1...
If it were actually the case women were inherently less interested in science, sure, I wouldn't care, but discrimination exists. Much more subtly than it used to, but it's still there, and hence still a problem.
The pronoun thing is probably a minor issue in the gender wars, though. That "he" is the default pronoun isn't a problem so much as, say, that the vast majority of scientists are men, which sends the message to young girls that science is not for them.
There's some interesting studies and anecdotes in this page: http://people.mills.edu/spertus/Gender/pap/node6.html