2004 Ford Focus, stick shift. When I take it out of gear at a stop light, into neutral, the RPM goes up to nearly 3,000 RPM. Why?

When first starting the car, just leaving it neutral, the RPM stays around 2,000. IT only raises when driving, as described above

Adjust the idle.

Like Anonymous says intake air leak OR a Throttle position sensor or Idle control valve. Take it to a dealer they will figure it out quickly instead of a lot of guess work at your expense.

A common cause of very high idle in that era Focus is a tear in the PCV hose where it bends sharply to follow the firewall.