As the auto-calibration is not done on the print bed itself, you only get a reference plane, and it is assumed to be the same as the print bed plane. Because of tolerances, this might not be true fore every printer. Read this thread for further information: Material squeezing out bottom of part
Short version: There is a z-offset option in every slicer, where you can compensate for such issues.
You should measure your filament diameter on multiple spots with a caliper and enter this value in cura. As stated by nopick, this might only be possible in the “expert” mode. The second important value is the value for esteps (how many step the extruder has to do to extrude 1mm of filament). You can set this value over the printer interface of cura.
See this howto regarding esteps calibration: http://reprap.org/wiki/Triffid_Hunter’s_Calibration_Guide#Measure
Use the command “M92 E820” to set the esteps to 820 or any other value you need. Don’t forget to do a “M500” when you are done, or your printer will forget your calibrated esteps value when you switch it off! You might also do a M503 to display you current values.