There's also the opportunity cost of the investment; the yield has to be compared to things like food stamps, education, basic research etc. There's a lot of low hanging fruit a well run government could be picking.
I would also tend towards the view that if the government invests like a VC it should take equity. If these companies genuinely have no other option, I don't see why this would be a deal killer. If they have VC they could take instead, the government shouldn't be offering free money.
The financial goals of this program shouldn’t be profit — or even break even. Any profit expectations will undermine the the way this program is evaluated.
If government wants an equity stake, they’d be better off investing in a fund of VC funds - like what the BC Renaissance fund does in British Columbia. They stuffed $100M (pocket change, I know) into a fund of funds and let the VC manage all of it.
Compared to the IRS? National security & intelligence? Social services? Monetary policy?
It's just not setup for making a profit.
On top of that, this is early stage funding and most of these companies will fail paying back little to nothing.
PS: Corporate taxes are down to 9% of the federal budget. They really don’t pay much in the way of taxes vs the services they benifit from.