In reality, it's because the Secret Service is for historical reasons the federal law enforcement agency most responsible for handling computer crimes. It's been this way since at least the 1980s, when the Secret Service was at the heart of the Sun-Devil Raids.
As anyone who's ever watched Law & Order can inform you: "two separate but equally important groups, the police and the district attorneys". In federal computer crimes, you can often substitute "Secret Service" for "police", and "US Attorney" for "district attorney".
As I understand it, the Secret Services' role in computer crimes investigations work is less central today than it was 2 decades ago, but they're still an important repository of investigatory talent for these kinds of cases.
Understanding that the Secret Service's involvement in the case was legitimate in no way means that you approve of the way the US Attorney's coordinating group for computer crimes led by Stephen Heymann handled the prosecution. That's a disclaimer I shouldn't have to write, but since this story is being voted rapidly to the top of the site, it's clear that I do need to write it.