I can cite two things that stations have done that prevents viewers from receiving their signals OTA.
First, many stations are not broadcasting their greatest potential signal. They are either not broadcasting at power levels below the maximum allowed by the FCC, including taking advantage of the maximum station exception, or they are not broadcasting from the best possible tower location.
Second, many stations have chosen to broadcast on VHF frequencies, or more astonishingly, low VHF frequencies. While understandable during the early days of the digital transition, as the inferior propagation of VHF was not yet fully understood, by the time the transition came to an end in June 2009, and stations had to make their final channel election, the inadequacies of VHF, and especially low VHF, were well known.
Other than those two things, much of the trouble with OTA reception is due to the nature of digital transmission itself, and more specifically with interference, not with the stations. Phoenix AZ and Austin TX (at least the eastern half of the market) offer near-optimal conditions for digital broadcasting, but Chattanooga TN and Pittsburgh PA have serious terrain challenges, and New York City and Chicago have man-made challenges to reception, which produced ghosts in the analog signal, but completely cancel out a digital signal.