https://github.com/atom/atom/issues/5246
Right, the font-size in the settings only changes what's inside the text editor. If you only want to change the font-size of the sidebar (tree-view), you could open Menu > Atom > Open Your Stylesheet and then paste:
.tree-view {
font-size: 14px;
}
You can't go too large since the line-height is fixed, but a couple px more than the default should be fine.