In general charities do not make taxable supplies - ie they do not sell anything that attracts VAT - therefore VAT tends to be a cost to them. Often a charity will set their shops (if they have them) in a separate legal entity and charge and recover VAT. The same thing applies to insurance companies.
I rent property to two different charities and I have to charge vat, they have to pay vat. as for the post on vat-in and vat-out on purchases and sales, don't forget the vat man gets 17.5% of your profit.
Irrecoverable VAT - the RNLI, like all other charities, does not trade and so cannot reclaim its VAT costs. Whilst we do receive some zero-rating i.e. VAT is not charged, in relation to lifeboats and station construction, there is still some £2.2m of VAT costs that cannot be reclaimed for costs that do not relate to the lifeboats themselves. These include, for example, Lifeboat station maintenance, Crew training, General crew and station costs, Prevention and education, Fundraising, and Support costs
The RNLI is currently campaigning to recover these costs and any help is most welcome.
We have yet to find out whether we can continue to use red diesel, since we should not be classed as 'private' boat users. However, if we are then we are able to recover any hydrocarbon duty paid so this should not be an issue.