Well first of all, there are significant differences between what McLaren was caught and found guilty of doing compared to what appears to be the case against Renault.
Secondly, it wasn't "really" $100 million dollar fine, because although they were excluded from the Constructor's championship, they could and did earn money for their final standings in the constructor's championship, and that was applied to the fine. So had they actually earned more points than Ferrari (which they fell two points shy of doing thanks largely to Alonso's "extended" pit stop during Q3 in Hungary), that would have meant the fine would have only been $50 million.
I have heard F1 budgets for some teams are well over $500 million a year. In F1's own TV program, "Inside F1" they reported that Toyota spent over $600 million in 2006 on their F1 program.
That said, even $50 million and certainly $100 million is a huge fine even for billion dollar companies, although I still feel McLaren got off relatively easy, and could have easily been banned from F1 if it were not for the fact that McLaren is a big part of the success of F1, and without it's participation, F1 would stand to lose hundreds of millions if not billions of dollars in revenue from sponsors, advertising, licensing, etc.