In the after show, The Talking Dead, someone speculated that the doc may be saving them for a cure, because in an earlier episode he speculated that a cure for the virus may be found someday.
Someone else noted that he has also been portrayed as a man of faith, so he has a giving heart and would definitely want to try to cure them one day if a cure became available.
He could also be part of a gubmint program and be required to keep them for some reason.
Maybe it's explained in the books... I'm not interested, but if you are...
http://www.amazon.com/mn/search/?ref_=nb_sb_ss_c_2_16&url=search-alias%3Dstripbooks&field-keywords=the%20walking%20dead&sprefix=the%20walking%20dead&rd=1