Hmm, my two Dish OTA tuners hooked up to one Hopper each provides OTA just as good as my TiVo and directly connected to my TV, which are all EXCELLENT PQ. If you have a very high end HDTV, the PQ might be a bit better directly from the antenna to the HDTV because your TV is getting the original source signal at its native resolution and using its very expensive electronics to process it compared to the fact that the Dish OTA module (and the TiVO) go through their own processing TiVo or Dish processing before leaving that box, and then into your television. While Dish and TiVo both seem to process VERY WELL, Dish does force you to choose an output resolution for all channels, so if you are tuned to a 720P OTA, but have the Hopper set to output 1080i, then your TV further processes it and displays it at the displays native resolution or YOU may be even further processing it through an A/V Receiver and further up-scaling it to 1080P, and there may be some noticeable, but very slight degradation due to the number of times the video has be converted and converted again in the chain. There are some purists who believe we are making PQ's worse, not better by this approach. I say, if one has good quality components in the chain, it results in better PQ. I can't say the same if one has crap equipment in the chain.
However, in cases of entry level or cheaper HDTV's, the PQ from a Dish module through the Dish box (and an A/V Receiver with a good processing chip) and out to your cheap TV can result in a noticeable IMPROVEMENT in PQ compared to connecting an OTA antenna directly into the HDTV, even with the many steps of processing and conversion.
Anyway, the difference between the Dish OTA module and connecting directly an OTA antenna into the HDTV should be of most minimal difference. I would consider getting an RMA for the Dish module if it is more than a slight difference.