Arthur Weasley's Ford Anglia was capable of invisibility:
"No one would see - this little button here is an Invisibility Booster I installed - that'd get us up in the air - then we fly above the clouds. We'd be there in ten minutes and no one would be any the wiser -"
Chamber of Secrets - chapter five - The Whomping Willow
And regarding invisibility and Muggles in general, in terms of the Knight Bus, Stan Shunpike sums it up pretty nicely in Prisoner of Azkaban:
"How come the Muggles don't hear the bus?" said Harry.
"Them!" said Stan contemptuously. "Don' listen properly, do they? Don' look properly either. Never notice nuffink, they don'."
Prisoner of Azkaban - chapter three - The Knight Bus
The Knight Bus isn't specially-magicked against Muggles; it's just that Muggles are out of touch with their surroundings. Stan's comment implies that should a Muggle "look properly" then he/she might be able to see the Knight Bus. However, wizards rely on Muggles' defensiveness, being unaware of the world around them (in general), and their wont to disbelieve anything they cannot explain to themselves (such as magic).
In the beginning of Prisoner of Azkaban, Harry is doing History of Magic homework, and he reads:
Non-magic people (more commonly known as Muggles) were particularly afraid of magic in medieval times, but not very good at recognizing it. On the rare occasion that they did catch a real witch or wizard, burning had no effect whatsoever.
Prisoner of Azkaban - chapter one - Owl Post
As well, the Ministry has a Memory Modification squad or program for those instances that a Muggle sees a magical vehicle doing most unMuggle-like things!
It would be hard to make all forms of wizarding transportation invisible. For example, to make all brooms invisible, as well as items like Sirius's motorbike and the Knight Bus, might be logistically difficult. Especially when you have wizards, like Arthur Weasley and Sirius Black, who liked to tinker with Muggle vehicles.