isn't this seemingly pro-women pro-science movie actually misogynistic?

Rating: 5/10 (30 March 2016)

Don't get me wrong, I LOVED this movie when i was much younger. That's why I came back almost ten years later an watched it again. Only this time, I saw many things I wasn't able to see before. And I am disappointed.
For example, through the entire movie, Ellie has fight off all the bureaucratic bullshit, embodied by all walks of men. Then the "love" would come to determine her fate, first by undermining her in the first round of selection - so she got bumped by some hypocrite; then by legitimizing her at the end by arms around her and telling the press that he believes her (then round of applause from the crowd), as if no matter how much she fights, she wouldn't get approved, but if a man comes to rescue, his one sentence would save the day. To make this symbolic pattern even more significant, was at the very end, the only character who gets Ellie's experience was a woman.
What's sad is that I don't know how much of these decisions in writing or directing was deliberate and how much of these sentiments towards women, especially women in science, are just so deeply rooted in our biases.