More likely not enough voters care for it to be a government priority.
You may well be correct, but that statement doesn't lead where you think it does. So I'd image that if you surveyed members of the general public on the matter you get the following response.
1. That most people would have no idea that small religious and non religious charities were treated differently by the Charities Commission - indeed I suspect most people wouldn't know what the Charities Commission is nor how charities are regulated. However ...
2. When they know about the different treatment most people would think it wrong and unfair that two charities with exactly the same income were treated differently and that the special privilege should go. But ...
3. That the issue shouldn't be a major priority and the government shouldn't really be spending its time one it.
But, of course the government decided back in 1996 to get rid of the anomaly so if the government devotes no further time or effort on the matter the special privilege goes. Why it is still with us is because governments over the years have prioritised retaining the special privilege and devoted parliamentary time and effort in bringing forward new regulations several times to maintain the special privilege
So the point is that although the public are unlikely to consider it to be a priority, the government has prioritised maintaining an unfair distinction over a quarter of a century after it committed to get rid of it, when all they would need to do to get rid of it is to do nothing, and they'd already committed to get rid of it in 1996. And while the public probably think it is wrong and should go but not a priority you can bet your bottom dollar that the lobbying power of religious organisations who have highly privileged access to government and parliament will be campaigning to make the government prioritise parliamentary time and effort to retain the spacial privilege.