There would be a very narrow (almost inconceivable) spectrum of circumstances that would make it advantageous to have a long gun in your vehicle and be at the location of, and in a position to do something about, a terrorist attack. There is also the concern that you, armed with a long gun, are easily mistaken for one of the perpetrators.
Having said that, there ain't a vehicle out there that cares about an extra 10 or 12 pounds of payload, so to my thinking, the only reason to not have a long arm with you is either laws that prohibit it in your state/city, or concern of theft. Me? Yeah, I keep something more than my CCW in my vehicles. But out here, it has a lot more to do with the probability of needing to dispatch a deer wounded by a vehicle than terrorists or other criminals. My county, like most very rural counties, would be a really poor choice to target. The population is quite low in density and extremely high in armament.
On that point, a long gun shouldn't be the only thing in your trunk. Jumper cables, a respectable first aid kit, flares (or the electronic equivalent), some water, a little food, a wool blanket, a heat source (sterno, for example), a multi-plier and a small assortment of hand tools are absolute must-haves in my book. The "trunk gun" is just another part of that tool kit for me.