Whilst I believe that with private school VAT the government are using tax as a subterfuge to deliberately remove education from children - which does go against their human rights - I can understand why the courts are taking the government's stated intent (to raise taxes to pay for state-funded services) at face value as a 'legitimate aim'
I also understand why they are setting the bar very, very high about what is 'proportionate' to achieve the aim of raising taxes even where it disproportionately disadvantages groups who would normally be protected from indirect discrimination (SEND, religion).
All taxes cause disadvantage to whoever is paying the tax, obviously! And as a society, we balance the disadvantage to the tax payers against the benefit to those recieving whatever the tax money is spent on (which may or may not be the same people, or with the same proportion of harm/benefit). That's never going to be exactly 'fair'.
It would be crippling if every tax resulted in legal challenge. The government of the day need a reasonable amount of leeway to do what they think is right, especially if it was in the manifesto.
There is a boundary though. We wouldn't allow, for example, a tax which was only applied to Jewish people - even if that money was used for really useful purposes.
These cases are testing the boundaries, and that's OK.
What I think will be interesting is if it goes on for long enough that it becomes apparent that no money is being raised, when you consider the increased cost of educating the children who move from parent-funded education to tax-payer-funded education.
Whilst the government will undoubtedly argue that their intent was a reasonable aim, will it shift that balance for the courts once it becomes apparent that the aim isn't being achieved and it's only bringing harm? Would a case be more likely to succeed at that point? A judgement against the government would still hugely damage future governments' ability to raise taxes, so I suspect the courts would remain very reluctant.