I don't know if you have much experience running non-profits, but giving an overly large one-time grant to an org which isn't necessarily prepared for it can be a fairly bad idea and often leads to the org doing mad yo-yo things and ending up penniless.
Spending money requires a certain amount of structure and process, and it takes a while to adapt to a money windfall. Going from a little money to a lot changes an org very significantly.
Granted, I also haven't looked much into the Rust Foundation, but I'm going to assume a $1 mio is significant for them. Google can always donate more down the road when the investment pays off and is digested usefully.
(Edit: The Rust Foundation had an income of $2.89 mio in 2022 and $2.56 mio in 2023 according to their annual reports. $1 mio sounds about right for what they should be able to usefully handle, from the gut.)