Are you doing this when booted from the CD?
It won't write to the root of the CD, you have to write the output somewhere else.

Right-click the hdb1-icon on the desktop and change to read-write mode, then do:
$dd if=/dev/hdb1 of=/dev/hdb1/bootsect.lnx bs=512 count=1

You should now have a file named bootsect.lnx in your linux partition.

Now you can format a floppy with: $ mkfs.msdos /dev/fd0
Mount it with: $ mount /dev/fd0
copy over the file: $ cp /dev/hdb1/bootsect.lnx /floppy