BlueZee is certainly right: if there's a diskette in the drive it has to be a bootable diskette! If there is no diskette in the drive, it means there's something wrong with the diskette drive (just disconnect to check that) or the cd-rom (same thing to do) or - much more probably - with the hard drive. To diagnose that, boot from your Windows 98 boot diskette (after setting boot from a: in the BIOS) and run the usual diagnostics (like fdisk, chkdsk, scandisk, dir or the diagnostic tools of the manufacturer) and repair tools (like fdisk /mbr or sys c:). I've had a case where simply doing a sys c: (putting the system files on the drive again) was all that was needed.
Hope that helps.