It had to stop and wait for a goods train which was going in the opposite direction (we saw that train go through the station in Austin - the line is single track around here).
Now you've discovered the joy of the American passenger rail network. As you experienced, nearly all of the passenger trains in the US outside of the Northeast travel on rails owned by the freight railroads. The revenue they get from a passenger train is far, far, far lower than the revenue they get from their own freight trains.
Your experience will vary depending on which railroad owns the tracks. For example, I took a trip from Chicago to San Francisco on Amtrak. The rails from Chicago to Denver are owned by one railroad, and the rails from Denver to San Francisco owned by another (the same that owns the tracks you rode on).
On the portion of the trip from Chicago to Denver, we stopped only for stations and crew changes. We passed train after train parked on sidings. After Denver it was a different story altogether.