I disagree. If it weren't for the trademark issue, the car would most likely have been called a GT40. That's like saying the 2009 Nissan GTR isn't a GTR because it's not a "Skyline GTR". Or by saying the retro Ford Thunderbird isn't a Thunderbird, or the retro Challenger isn't a Challenger, or the NSX isn't an NSX because it's a hybrid, etc...
Semantics aside, the Ford GT is the successor and part of the GT40 heritage. It's technically incorrect to call the 2004-present cars "GT40"s, it's not entirely appropriate to discount the lineage.
The fact is the 2005-2006 Ford GT are officially called "Ford GT" and not GT40 regardless if you approve or not. It is not disputable. No one is disputing the heritage as I already said that the Ford GT is a homage to the GT40. I have not met one single Ford GT owner referring his cars as GT40.
Steve