Isn't M$FT a $Trillion dollar company? They can afford it on their own bootstraps
Granted, a project like this probably doesn't strictly need all $1 billion all at once, but I'd argue it's better to get whatever necessary funding upfront instead of risking having sunk a partial investment without being able to obtain the rest should the company's financial situation change.
My assumption is that the real reason this is a loan from the government and not paid directly by Microsoft has to do with other factors, like Microsoft not waiting to be in the hook for the billion dollars if the partner company folds, or the potential for loan forgiveness, or other incentives that make the effectively loan cheaper than cash.