http://www.statesman.com/news/conten.../0223wear.html
If Ben Wear was half a journalist he would have researched the story before posting it.
There are two parallel UP corridors between San Antonio and San Marcos, so the biggest quarries around New Braunfels have no impact on commuter rail. The Austin White Lime plant at McNeil Junction is also served by Cap Metro, and the UP line near the quarry north of Round Rock is not planned to be used by the ASA - they plan on using the MOKAN corridor instead.
ASA projects that after rail relocation, local freight traffic will go down to around 10 trains per day from the current 25-30 trains per day. That's enough freight traffic that the time separation being used by Cap Metro will not work, but not enough to preclude commuter rail if FRA compliant train sets are used.