I'd initially be wary of using a neoprene lens "cap" for physical protection unless it was at the end of the rigid hood because it seems to be too flexible to stop something pushing against the lens element. My opinion might be different when I actually see one in the flesh.
The front lens element is a protective element and may be relatively cheap but it won't be very cheap because it is not simply flat glass and so it is still worth protecting with a sturdy lens cap. The Don Zeck would seem to be the best for that.
If the 500mm lens hood works like the 300mm lens hood then the Don Zeck cap should fit on the lens with the hood on or off and should also be fittable and removable while the hood is on or off. Anything that straddles the end of the lens barrel rather than fitting inside it may interfere with the rigid hood or may require the rigid hood be removed in order to fit or remove the lens cap.
I've got an OpTech (I believe) 120 mm cap for my 300mm f/2.8 IS. It's pretty rigid and offer great protection but only on the lens barrel. For my 600 f/4 IS I bought a LensCoat 178-197mm neoprene cover.
With its hard piece installed it looks like it's going to offer excellent protection. Best of all it fits either the barrel or the hood. With the hard piece removed the LensCoat gives less impact protection but offers good dust protection that can be folded and stored in a jacket or pants pocket. It's new so I don't know how long the tight, stretched fit will last.
For the cost of this lens, I would want a rigid front cap. The standard Canon cap takes a lot of criticism for usability but it offers excellent protection. The Zeck cap is as effecitve in protecting the element, it is solid and fits within the lens lip which means it works with either the hood in stored or shooting position since it does not come in contact with the hood. Plus it has none of the usability issues of the Canon. It sounds like the Lenscoat Hoodie also has a rigid insert but since it is made of neoprene like the Optech, you either stretch it over the lens lip or either end of the hood. Maybe it fits well, but it can't be the same precise fit as the Zeck since they attach differently. Here is a review of the Zeck including a link to his site showing exactly how it mounts to the lens:
Your other alternatives seem to be the plastic lids. There is a kitchen place that sells 2 size lids, one to fit the hood and the other to fit the lens. Its a cheap solution but how much protection can that offer? I guess it works if you only care about dust but it is not thick/rigid like the Zeck.
Zeck - most protection and best fit, great usability/durability
Lenscoat Hoodie - best bang for buck
tupperware - better than nothing
I use the Op Tech hood hat. I've added a rigid insert which I cut from a cheap plastic cutting board. It would be simpler to just buy a Hoodie in the first place.
