“High speed rail” means intercity rail (think airplane or Greyhound bus replacement), not commuter rail or metro rail. That makes sense to put along a freeway because there’s generally only one direct freeway connection between each pair of major metro areas.

I agree that it doesn’t make sense to put commuter rail or metro rail adjacent to a freeway. Ideally, it would be the opposite: the routes radiating from the city should have the freeways and rail lines spread as far apart from each other as possible, so that commuters in different areas have good access to either one mode or the other, rather than some having good access to both and others neither.