Title is misleading. Google didn't pay up front to keep the search bar, but rather agreed to share a percentage of the revenue generated, which ended up being $1B.
why? It's effectively the same thing, except the risk profile is different. The resulting revenue wasn't a complete mystery so they probably knew the deal equaled about 1 billion.
But the deal wasn't Google giving Apple $1B to be the default search on iOS. It was Google giving Apple a 34% share (perhaps - it's still a bit unclear in the article) of iOS search revenue. It is still a deal worth ~ $1B, but not a deal for $1B.
The context is important. If the number is 34%, then Google's iOS revenue would be around $3B, of which Apple got a cut.