Ian,
as someone mentioned, it's like comparing Mazda to Lexus. Both are worse than M1 Abrams
Kidding aside, the difference is in design, manufacturing, quality control and tradition. Zeiss is a company with deep scientific roots. Every lens that they make have gone through a lengthy design phase, where engineers made sure that what they had created on computer can be actually manufactured. They use optical glass of superb quality, their manufacturing facilities are state-of-the-art and quality control is outstanding. You can pretty much get any Zeiss lens and expect it to perform well. With any other lenses you're playing lottery. Variation from batch to batch can be also significant.
Exception is Leica and some Canon "L" series lenses. It's also Zeiss's tradition to make good products. As they say "superior German engineering". They built that reputation over a century and their products stand by it.
Look at most other manufacturers - you have to know which products are even worth looking at, not to mention buying!
A lot of 3rd party lens manufacturers started using advanced materials (like aspherical lenses, fluorite elements, ultra low dispersion glass, newer type of anti-reflective multicoating, etc). However, all this is just bells and whistles. It takes skill, experience and know-how to design AND produce a lens that would benefit from these materials. It takes great manufacturing tools to properly assemble it and test it. And it takes even more to stand by it (how many lens manufacturers out there will be even willing to repair your lens after warranty period is up?). So, using advanced materials and super-duper-new-computer software has nothing to do with final product. If it's not done right, it won't be anywhere near the blueprint specs.
People working at Zeiss are like craftsmen. They know exactly what they're doing and that's why they make such excellent products. Here is also another hint - most of successful lens designs offered by other manufacturers are clones of Zeiss design.
Mike.