Several reasons...
The EF 100-400mm f/4.5-5.6L IS USM II is a fantastic lens... staggeringly sharp and the sharpest and best performing lens in it's class... beating out even all the 150-600mm lenses on the market. It is so sharp, that when you add a Canon 1.4x III teleconverter to take it to 140-560mm ... it is *still* sharper than all the 150-600mm lenses on the market. It is *that* good.
I do NOT own the 200-400 (because I made other life choices... like being able to afford to have a roof over my head). However...
It isn't just a "200-400"... it's a 200-400mm f/4L IS USM Extender 1.4 ... that's a lot so I'll break it down.
The lens can provide a constant f/4 aperture all the way through the focal range. The 100-400 f/4.5-5.6 is a variable focal ratio lens and it can't provide f/4 at any focal length. It's basically about a full stop faster all the way through the 100-400 range.
To be a stop faster, means it needs a larger aperture, which means it needs physically larger glass elements. Those elements don't just have a larger diameter... they're also thicker. This, in turn, increases chromatic aberration of the optics, necessitating the use of more exotic glasses or more corrective elements to combat the chromatic aberration (the effects of "dispersion" of different wavelengths of light at different angles). Straight away, that makes any lens more expensive (noticeably so). It's why you see a huge price difference between a 70-200mm f/4 lens and a 70-200mm f/2.8 lens.
BTW, at these longer focal lengths with bigger apertures... and the need for exotic "glass" materials to make the lenses... Canon turns to things like fluorite crystal. Fluorite is a "low dispersion" glass (so you can focus light with reduced effects of chromatic aberration). But the problem is, while the crystal does occur in nature, it is always flawed and doesn't naturally occur in crystals large enough nor clean enough to make a lens. This means Canon has to "grow" their own crystals. You can "grow" a crystal in a kiln. But the problem here is that if you try to "grow" the crystal too quickly, you'll get internal flaws that make it unsuitable for optical use. So it has to be done very slowly. Depending on the size of the crystal needed... it can take weeks to months to grow the crystals. You can only grow so many at a time per kiln and you need a lot of these kilns. This *really* drives up the manufacturing cost.
Second... the 200-400 also has a built-in 1.4x teleconverter. And it's not just a generic teleconverter... it's optimized and tuned specifically for THIS lens. That means when you flip in the teleconverter, the focal length changes while the lens maintains optical quality without the discernible loss in "sharpness" normally experienced when you use a teleconverter. In other words, this becomes a 280-560mm f/5.6 lens.
Finally... the market demand. A lens like this wont exactly fly off the shelves (it would if it sold for around $2000 but it costs more to make it). That means all the expense of the R&D and manufacturing equipment needed to make this lens, is spread across significantly fewer customers... driving up the price tag for those who really want it.
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