A few more tidy ups. Firstly thanks for the praise factor-fiction but I'm really not a tax expert. I do a bit of it here and there, mainly Corporation Tax not income tax and need to have a decent knowledge of the system in doing my real job which is as an auditor.
buildersmate has, not surprisingly, pretty much covered everything else already. You cannot claim petrol or mileage rates for travel between home and work. Doesn't matter if you are an employee, self employed or indeed in an owner-managed company. You can't do it.
Also Chrissa is wrong, don't follow that advice. Whether you are VAT registered or not (which I guess you are not as you describe it as "small") you cannot reclaim VAT on fuel if the fuel expense itself is not deemed a business expense. Even if you could, you'd have to account for a scale charge for private mileage anyway.
You can only claim motor expenses of any sort if the vehicle is used in the business. If it's used to go and get stock from wholesalers or deliver goods to customers then that's fine. Expenses in relation to that would be allowable. If it really is only used to go to and from work then nothing relating to the vehicle is allowable. You wouldn't be able to claim the road tax, insurance or any repairs either. And you wouldn't be allowed to claim capital allowances on the vehicle if you own it or the lease charges if you don't.
It's not clear what exactly is meant by "the van is purchased through the business" in the OP? If that just means payment comes from the business back account then that's irrelevant. It's presumably charged against Drawings or Directors loans depending on what the structure of the business is. If it is meant to imply the costs of the van itself are allowed as a business expense then that seems odd. If the accountant is allowing the costs of the van then it must have some business use. That being the case then some of the running costs would also be allowed.
It may just be we're all reading too much into this and all itsmefolks is actually saying is "why doesn't my accountant let me claim the petrol costs from home to work?", in which case the answer is because it's not business mileage and isn't for anybody.