I did not find anything to allow me to exclude a user or users from the backups when using cpbackup so I made a couple modifications:

1st. I create a file called nobackup that contains the users I do not want to backup. One per line.

2nd. I created a script (I named mvuser): This script will take the users in my nobackup file, move them out of the /var/cpanel/users directory. This way when cpbackup runs it will not backup those users since it uses the users from the /var/cpanel/users directory.

3rd. This is the way I implemented it. I modified the cpbackup script but you could simple execute the mvuser script before and after the backups are completed.

Code:
#!/bin/sh

# mvuser - script to move users from /var/cpanel/users during backup
# process. We move uses out of directory we do not want to backup
# Script takes 1 argument. Either in or out.

# Place the following two lines below the following line /scripts/cpbackup
# close to line 280. Remember to remove the comment on the system line
# sub backupaccts {
# Move the users in nobackup back to users directory. See mvuser
# system("mvuser out");

# And the following two lines before the closing "}" for the sub backupaccts
# close to line 346. Remember to remove the comment on the system line
# Move the users in nobackup back to users directory. See mvuser
# system("mvuser in");

USERS=nobackup     # list of users not to backup

DIR=/var/cpanel/users
TMPDIR=/tmp

case $1 in
        out) # move the user file out temporarily
                for i in `cat $USERS`
                do
                        mv $DIR/$i $TMPDIR
                        echo "mv $DIR/$i $TMPDIR"
                done
        ;;
        in) # move the user file back to DIR
                for i in `cat $USERS`
                do
                        mv $TMPDIR/$i $DIR
                        chmod 644 $DIR/$i
                        chown cpanel:root $DIR/$i
                done
        ;;
        *) echo "Usage: mvuser [in/out] ";;
esac

#
# End
#
Note: the mvuser script takes argument in and out. Out to move the users from the /var/cpanel/users and in to move them back in. So I simply have the cpbackup script execute mvuser out before I start the backup of the users and mvuser in when the backups are complete.