Well, you are right in that the boot-time scanner is no prevention.
It might be handy, however, to remove the infection if it already got to your computer (no protection is 100%, and there's a lot of new malware appearing every day, so it sometimes may happen). Since it is started before (most of) the malware has chance to activate, it's more likely to be able to remove it easily.
As I said, however, making a boot-time scanner for Windows 98 would require "back-porting" our scanner to the DOS environment, which is really hardly worth the effort.