Sorry, I only seem to have confused things :(
Let's go with your example:
You have sales of £48,000 (makes the sums easier) and costs of £2,500 on which you pay VAT at 20% ie £500.
If you are not registered for VAT you invoice your customers £48,000 and pay out £3,000 to your suppliers for a profit of £45,000.
If you are registered for VAT and so are your customers, you invoice £48,000 plus VAT of £9,600, and pay out £2,500 plus VAT of £500. You have a profit of £45,500 so you are better off by £500, 20% of your costs.
But if your customers are not registered for VAT they are not going to accept you costing them 20% more (otherwise you could just stay unregistered and raise your price), so you have to drop your net sales to £40,000. You invoice £40,000 plus VAT of £8,000 and pay out £2,500 plus VAT of £500. Your profit falls to £37,500 - ouch.
But here is the best bit - if you can opt in to the flat rate scheme you may be even better off. Different percentages apply to different trades, so if your trade is journalism, a rate of 12.5% applies (this is reduced by 1% as an additional incentive in the first year, but I'll ignore that for now).
In this case you invoice £48,000 plus VAT of £9,600 ie £57,600 but you only have to pay 12.5% of £57,600 to the VAT man so you have net sales of £50,400. You pay out £3,000 in costs (you can't claim the VAT under the flat rate scheme) so you have a profit of £47,400. The VAT man has paid you £2,400 for doing a bit of paperwork!