When you file your VAT return for fares you can deduct your VAT outgoings such as petrol, car repairs, expenses associated with running your business etc so you don't have to give 21% to the tax man.
If a business ( company or otherwise ) is carrying on both exempt and VATable activities then they would have to be registered for VAT if over the relevant thresholds for the VATable business. A good example here would be an undertaker / publican ( of which there would be quite a few around the country ) Undertaking is VAT exempt. If there were items of shared costs, e.g. one ESB bill for the whole premises then the portion relating to the VATable business would be claimed as an input credit. The VAT on the portion relating to the undertaking would not be claimable, as that part of the business is VAT exempt. In both cases of course, the charges for ESB are tax ( income or corporation tax ) deductible. One cannot, and should not, attempt to claim VAT on anything to do with a VAT exempt activity.