Took 3 yr old to dr said ear was pink and throat was pink. running fever and complaining about stomach. is this a virus or sinus infection.

Viral likely: Viral infection is the most common one causing upper respiratory infection.

The doc said ???: What you've described fits with a kid who doesn't like his/her ears looked at (pink) and some throat irritation.You didn't mention anything that would point to sinus disease. The scene as described could be a simple virus or more, but i would defer to the doc who actually had a look. Exam is the best way to put it together.