The reason is usually simple. The TV maker doesn't have the patents (like Sony) and one of the HDMI HDCP rules is to protect the HD content. Since passing the HD content could open it to copying they simply don't.

If you must pass HD audio, shop for models that do that. Mostly Sony from what I've experienced.

-> That out of the way, the accepted setup is all sources to the receiver which does the HD audio work and passes the HD video on to the TV.