If this is the way you altered it that should be fine as you removed font-size: 11px in #navigation a which does make the navigation links larger than the rest. If you plan on doing more theme editing stuff, you should get yourself Firebug, an awesome tool to analyze the style, structure and scripts of a website.
Remove the font-size setting from #navigation a and play with the margin and padding values of #navigation a and #navigation li in your theme's styles.css