The 100-400 is a zoom while the 400 is a prime and the conventional wisdom is that primes are usually considered to be optically better than zooms.
In practice
with these particular lenses there's very little difference ... so in this case you would be pretty much correct in thinking that the 100-400 zoom can do everything that the 400mm prime can do and more.
The same doesn't necessarily hold true for cheap zooms versus cheap primes. One of Canon's cheapest lenses ... the 50mm f/1.8 ... is optically excellent. It's miles ahead of any of the budget "superzooms".
I own the 100-400L and have used the 400 f/5.6L and I prefer the zoom, mainly because of (as you've noted) the added versatility of being able to zoom and the fact that it has image stabilisation where the prime doesn't.
Here a picture taken with the 100-400 ...
http://www.flickr.com/photos/andy_keir/2031055421/