Above all else what Shelby needed was someone with a lot of money that would provide the support for research and development. GM had the Vette and didn't need the competition and didn't want to spend the money. I suspect Donald Healey wisely turned down Shelby mostly from a financial standpoint, it's not like he was loaded with money. Ford was the perfect 'mark' (someone said one was born every minute), uh, er, 'Marque' (a brand name, especially in the automotive industry) I think I mean...
It was a big risk, but paid off well for Ford in the long run.