Those jobs wouldn't be there without the US company that is Amazon. Having Amazon invest in the UK is a net win for the country. In addition to corporate tax, they likely also pay indirect taxes, such as business rates on property, stamp duty, and (some) VAT.
If you were to flip this, I take it you prefer a company such as BP pays all of their tax in the country they operate in, and very little in the UK? Most assets are not UK based, after all. That's the same reasoning.