To set the minimum font size in Chromium (Linux), you must edit the ~/.config/chromium/Default/Preferences file:

gedit ~/.config/chromium/Default/Preferences

Look for this inside the file you just opened:

  },
"webkit": {
   "webprefs": {
      "default_fixed_font_size": 15,
      "default_font_size": 16,
      "fixed_font_family": "Monospace",
      "sansserif_font_family": "Droid Sans",
      "serif_font_family": "Liberation Serif"
   }
}
}

And add this two lines under "webprefs": {

 "minimum_font_size": 16,
"minimum_logical_font_siz": 16,

Thanks to Mahdi for the tip!