The problem isn't with the Windows side, its with the iOS side. If iOS doesn't get a proper connection with the host computer, it won't charge. USB wall adapters allow a charge because they provide a small level of power to the data lines, allowing the iOS device to charge. Ever since the iPhone 3Gs, iDevices will not charge if giving 5 volts on just the power leads on its USB plug. On Mac and Windows with iTunes installed, iOS makes a proper connection to the desktop OS and initiates a charge.
Do this: Find a Windows computer that had iTunes installed, but has never had an iOS device plugged in. Let's pick Windows XP. You plug in your iPhone 4S, the little New Hardware balloon pops up. It says "New Device found...", (a few seconds/minuets), "Apple iPhone", at the point when it says "Apple iPhone" the iPhone starts charging. Not a second before. Why? Because iOS has yet to make a connection with the host OS.
The brick wall though is that the OP is using Windows 98... Legacy os which leads me to think legacy hardware which is far less flexable.
It would be a nightmare to support such an old OS as if iTunes isn't bloated enough already (I still have an early version bundled on a Mac OS 9 disc. 2.2MB...
Back to the Windows issue, I quickly combed over such smaller details about limitations of earlier USB implementation and Windows. It's rather late but there are some rather obvious replies and some conflicts...
When it comes to iOS and power requirements, there are some oddities when using AC chargers etc. I remember my third gen iPod Touch (32GB model based on 3GS iPhone hardware) and despite having my handy charger included with my iPhone 3G (green dot replacement) My iPhone would charge just fine. The iPod on the other hand struggled with the charger causing the battery icon to rapidly flicker between it's charge level and the "charging" icon.
The problem? not enough amps (but enough to trigger) charging it despite exchanges and even buying another charger from Apple. The odd part, my old PowerBook G4 never had a problem with it. Other USB oddities, an older charger that I bought for my 5th gen iPod. I also used the same charger to recharge my Xbox 360 controllers with the battery packs installed. On the other hand, it lacked the power to recharge a PS3 controller. The older SIXAXIS models nor the DS3. The Nintendo Wii does just fine though for that. ;-)
When it comes to the legacy PC and older operating systems such as Win98, hardware control was rather limited due to many different changes over the course of the life of the OS. Moving to the purposed Standard "ATX" form factor but with so many different vendors (The 440BX mainboard design was ideal but expensive so many others showed up along with AMD and the K6-2 and eventually the Athlon.
These board designs during that time were mixed, some great, some just evil... and due to the partial reliance legacy design, were far less flexable to control from the OS directly other than some high end models later on that were overclockers dream machines other hardware, such as USB 1.x had it's limitations in hardware.
Onto the scenario of installing iTunes onto a PC but yet never connecting an iOS device to it. If iTunes is already installed, the system hooks are already in place regardless if an iOS device was ever used at all.
lets complicate things a bit, say you never updated iTunes and the iPhone 5 is ready to plug in but you never updated the software, of course it's going to charge as the pins for the dock connector remain a constant. for +5 volts DC and ground if the device has changes internally for power and the newer software doesn't know how to properly address it, of course you're going to see problems as the proper system hooks are not in place...
If iTunes isn't installed at all, most likely you will have unknown hardware in your device tree and something leaching current from the system. It needs power to be recognized by the OS and the proper driver for the system to understand how to use it. In the case of Win98, typical bare bones basics are a .vxd and .dll package. since none exist, it would be seen, but not understood.