Well, this is somewhat the crux of the issue. Someone did mention to me that the Ft. Hood proclamation was for civilian casualties not the active military personnel, however, there were 13 killed, only one was a civilian, so it was done just for him? Somehow, that doesn't seem like the reason.
According to the US Dept. of Veteran's Affairs website on the guidelines of a proclamation to fly the US flag at half-staff, the first thing listed is "when a whole nation is in mourning". There is a list of annual days for half staff, Memorial Day, Patriot Day, Pearl Harbor Remembrance Day,etc. There are the standard incidents for national mourning, the death of a president, former president, vice president and former, chief justices, speaker of the house and the like. The president can proclaim in the event of other officials, former officials, foreign dignitaries and other tragic events.
The foreign dignitaries have been somewhat rare but it explains the proclamations made for Sadat, Rabin, King Hussein, Pope John Paul II (though I guess one could argue he is a religious figurehead not a dignitary) and Nelson Mandela.
The other tragic events leaves things wide open and doesn't really distinguish that it should be limited to just civilians or excluding military personnel. Hence, the proclamations for Boston, Sandy Hook, Oak Creek, WI, Aurora and Tucson. I would say those were tragic events that fall under the "national mourning". So, did the Washington Navy Yard, while the deaths were civilian employees or contractors, it is a military base with military personnel on site. Ft. Hood had one civilian casualty, the rest were active military. Both happened here at home where you would hope the service men and women would be safer. Not that any soldier's loss isn't sad, it is an unfortunate possibility of those in combat or hostile zones. Mass deaths due to hurricanes, airplane crashes or other accidents are also tragic, but they are not directly due to premeditated violence like the incidents that have been given the half-staff honor recently.
Given that a precedence has been set, I think it is a fair question as to why Chattanooga has not been included and for that matter though I didn't see any call for it, Charleston, I'd say that it hit hard as well. There is actually more precedence since one of those victims was a a South Carolina state senator could be considered one of those "other officials". Perhaps because it happened at a church and right now there seems to be a lot of disdain for religion and religious beliefs, so maybe they decided to keep it separate.
Btw, did the WH Press Secretary give an explanation? Perhaps, since it is considered to be at the president's discretion they don't feel a need to say why or why not on any decisions.
Anyway, my main complaint was those complaining about those that were just asking why it was being excluded from what seems to have become a trend of doing it for these mass rampages. The gesture doesn't change what happened, it's just that it has kind of become an outward showing of support and solidarity through these horrific acts. The country is so divided on so many issues, anything that shows a united front in my view certainly couldn't hurt.