aaand many Cargo packages do use it, right now. It became an inseparable part of Rust ecosystem. You cannot build any embedded program or something slightly complex (omg Protobufs!) without build.rs. Not just your own program but all of your dependencies' build.rs is also executed.
I get the need for simple ways to make ecosystem inviting to the new developers. However, I think Cargo was completely mis-designed for simplicity only, where a system language like Rust should shine in its ability to control complexity. With the bad initial design, they invented hacky solutions like build.rs which speaks a string-based language to talk with Cargo!
On top of that crates.io is completely ripe for typosquatting and package overtakes. I think the ecosystem should be completely revamped to a Maven-style namespaced repos and it should require strong GPG signatures.