In this case, "Engine" could mean just the basic football elements. I wouldn't mind it, as long as the engine is good to begin with. And just like someone else said, SEGA used the same engine in NFL2K5 that they did with NFL2K for the Dreamcast.
Generally speaking, what you just said is correct. The engine is the core and has little to do with graphics. For example, games like Far Cry are still using the "Unreal" engine which first came out in 1998 or 99. The engine has evolved but the core is still the same. And yet Far Cry looks and plays a lot different than Unreal so I wouldn't worry about it. In programming terms the engine is the main basic elements that you build upon. And yes the 2K engine was the same throughout the series, although it did receive a significant evolution for the 2K4 version. Madden's did too, remember how different 2004 felt from 2003? The differnce with Madden is that the visuals weren't changed.
The point is the same engine can produce SIGNIFICANTLY different games so we shouldn't worry just yet.