UK Government Coronavirus Job Retention Scheme Funding
It is not correct to say that the Coronavirus Job Retention Scheme is essentially providing loans.

A little background.  The UK government currently has two major schemes to support businesses and through them their employees: the Coronavirus Business Interruption Loan Scheme for small / medium businesses together with a similar scheme for large businesses, and the Coronavirus Job Retention Scheme.

As their names suggest, the former is a loan scheme, the latter isn't.  As you imply, the cost to the government of the Coronavirus Job Retention Scheme will have to be funded somehow, probably initially by extra government borrowing, but perhaps eventually by increased taxation. Depending on the form of taxation, some of the burden of that extra taxation might fall on the businesses and/or employees who benefited from the Scheme. 

However, there is no reason to expect that there would be any close match, at the level of individual businesses, between their receipts from the Scheme and any extra taxation they might have to bear.  Corporation Tax, for example, is subject to complex rules which bear little relation to eligibility for receipts under the Scheme.  It would not be correct therefore to regard the Scheme as offering loans with an expectation of repayment.