There are many factors that go into the quality of a digital camera. Of course optics are huge. Apple has done a lot of work to make their optics in the recent iPhones quite good for their size (if you shake the phone, you can hear a rattling sound, it's the way they have their optics with multiple lenses). Heck, you can even get crazy things like this:
iPro Lens System
However, even more important, if you at least have ok optics is that ccd sensor(s). High end cameras often (or used to) have multiple sensors, one for each of the primary colors. This lowers noise, and gives higher image quality. Another factor can be ccd size. A larger ccd allows more light and thus more "signal". Larger ccd's are often better at producing clearer low-light images.
Obviously, cell phone makers want to make their components as small as possible, as energy efficient as possible, and as cheap as possible. So these factors are typically diametrically opposed to the needs of professional photographers, who usually care more about quality than they do size, weight, cost, etc.. It's all about priorities.
In the consumer space, it's all about Megapixels, because it's an easy statistic that consumers can recognize. Also, having a large number of megapixels means you can resample the image to reduce noise and improve the image quality digitally to a certain point. Megapixels alone are pointless if they don't also come with the ability to better utilize them.
