What is the End of Train Device RF Path?
Let's use one of the many online link budget calculators to get a rough idea of received power of the free-space path over 3 miles:



We have just under -60dBm at the receive end. That's still a fairly strong signal - people with good hearing can discern -60dBm on a good crystal radio.

This is partially due to the relatively high 8W transmit power level - some end of train devices use compressed air from the train's brakes to generate electrical power for the radios.

But your instinct is correct - in spite of the "easy" link budget, end-of-train devices do encounter dead spots along a route where the link does not work - it's part of the statistical nature of mobile communications.  

Back to your question, railway operators typically use a repeater at known bad spots (e.g. tunnels) when it's important to keep the link working.