Code:
$ awk -F"," -v OFS="," '{ for (N=2; N<=NF; N++) if (!$N || ($N==" ")) $N=0 } 1' data
Wed Feb 01 09:00:02 EST 2012,0,0,0.4,0.3,0,0.3,0,0.3,0,0.5,0,0.3,0,0,0.4,0.3,0
Wed Feb 01 09:00:11 EST 2012,0,0,0,0,0,0,0.2,0,0,0,0,0,0,0,0,0,0
Wed Feb 01 09:00:22 EST 2012,0.7,0.4,0.5,0.4,0.3,0.4,0,0.4,0.5,0.6,0.3,0.4,0,0.1,0.5,0.4,0
Wed Feb 01 09:00:42 EST 2012,0.9,1.0,0.6,0.5,0,0,0,0,0,0,0,0.5,0,0,0,0,0
Wed Feb 01 09:01:02 EST 2012,1.0,0.8,0,0,0,0.6,0,0,0,0,0,0.6,0,0,0,0,0
Wed Feb 01 09:01:22 EST 2012,0,0.7,0.7,0.6,0.5,0,0,0.5,0,0,0,0,0,0,0,0,0
Wed Feb 01 09:01:42 EST 2012,0.9,0.6,0.6,0.5,0,0,0,0.4,0.7,0.7,0.4,0.5,0,0,0.6,0.5,0
Wed Feb 01 09:02:02 EST 2012,0.8,0,0.5,0.4,0,0,0,1.1,0,0,0.3,0.4,0,0,0,0,0
Wed Feb 01 09:02:22 EST 2012,0.9,0,0,0,0,0,0,0.7,0,0.6,0,0,0,0,0,0,0
$