I just upgraded a few minutes ago, and immediately noticed the font change. My preferred font from PyCharm 2016.3, "DejaVu Sans Mono" is still selected in the font settings dialog. However, PyCharm is silently substituting "Monospaced" instead.
The problem seems to be specific to DejaVu Sans Mono. Other fonts seem to work fine in 2017.1. The older PyCharm is still working correctly.
I even tried removing DejaVu Sans from the system fonts and putting copy in my local user fonts (~/.fonts) folder. That didn't help either I solve this my using
mirror font tool for this IDE/Editor.
Other fonts in the IDE (labels, buttons) are different as well. I'm on Mint 17.3 (Ubuntu 14.04).