Depends. Plastic is not as good of a barrier to air than glass so, over time, air will find its way into the plastic carboy and oxidization will occur. How long are we talking? Who knows. If you're only in secondary for a week or two I don't think it would matter (read...I'm not a scientist). Just make sure you clean it well in order to get the nasties out of any scratches that may be on the inside of the carboy.