2) Granted, there are some arbitrary restriction on cars, but they are still a lot more open than software. You can easily alter them, fix them yourself, etc. None of that is remotely possible with commercially-distributed software. I can't just fork Tweetbot, add in support for Orkut, and redownload it to my phone. However, if I want to install a better radio into my car I can. Software (especially on mobile) exists as an immutable "black box" that you have no access to other than the user interface, and that makes it less valuable.
3) No one is arguing that it is inherently wrong to charge for software. People refuse to pay not because they are principally opposed to it, but because the average price of an app in the app store is far below $.99, and thus $.99 seems like an inflated price.
4) It's true that apps like Photoshop are valuable, but it's apparent that their prices are absurdly inflated. Pixelmator can make an app with 90% of the functionality at a little over 2% of the price. Is that 10% extra functionality really worth all those hundreds of dollars? For most, it isn't. The same can be said of apps. Sure, that $.99 app is cool, but this free one does 90% of what the paid one does. Is that 10% extra functionality really worth all those dozens of pennies? For most, it isn't.
When designing a new car, a lot of money goes into research and development, money that cannot be recovered (sunken costs). However, once that's over and the assembly line is put together, the cost of creating new copies (while never zero) it definitely converges to the cost of the raw materials involved. The more items the assembly line produces, the cheaper it gets. And when buying a car, you're paying a lot more than that, because you're in fact buying a brand, not just some pieces of metal put together.
I also disagree on a car being "open-source". Assuming you can make copies of your car and give those to other people, you'll be obliterated by trademark, copyright and patent lawsuits. Also many car manufacturers are voiding your warranty if you go to unauthorized car repair shops. And if you can look under the hood, that's only because of strong consumer protectionism laws.
Apple has more than 50% profit margins on iPhones. Is that moral? Well, they need to earn a profit (otherwise they wouldn't be in this business) and they also need to pay the research and development costs for newer versions or for other products. And after all, this is capitalism - if you don't like it, buy from somebody else.
So why can't this rationale also work for pure software? After all, the developer needs the profit to develop newer versions, improvements or other applications from which you may also benefit. And again, this is capitalism. If you don't like it, search for something cheaper, or create your own.
RMS's principle (being paid only for creation of software, not for delivery of copies) does not work because it doesn't scale. You cannot put together an assembly line for software, like you can for physical products. This effectively means that you end up selling your time, which makes a good living, but it won't make you rich and it won't allow you to work on lots of silly things that may or may not pay off.
Also, only simple apps can be cloned easily. No software can currently match Adobe Photoshop, which still deserves every penny, and it wasn't for a lack of trying. I use Gimp because the price of Photoshop is too high for my amateurish needs, but I would shell out the cash for Photoshop in a heartbeat if I would be a professional photographer or designer.
The $.99 price tags is common just because the app stores are filled with crap, with most apps not even deserving $.99 - but create an app that enriches people's lives and even allows them to make some money, and you'll have no problem selling it for $90 or even $900.