why did the Batmobile

Because the design is different.

Can't stop the signal.

Even though the Batmobile in Batman Beyond's timeline can fly like a jet, I figured it would still be considered a "car" like all the other hover/flying vehicles people were using in the future Gotham City. Thus, since Bruce Wayne would be using the Batmobile to navigate around Gotham, it's still his "car." If he's planning on zipping between buildings and lanes of cars, the Batmobile doesn't necessarily have to go incredibly fast.

Perhaps Batman has a separate Batwing that would be more comparable to other futuristic aircraft instead of the futuristic "cars." Maybe by this time the Batwing is a full-on stealth aircraft or something like the Javelins that the Justice League used that're more focused on speed instead of maneuvering around Gotham City.

Can't be too careful with all those weirdos running around.