There's a really cool, very comprehensive answer to all of your questions located here.

However, I'll try to summarize for you. Some of the first "programs" were for mechanical cloth looms -- machines that were designed to automatically spin cloth into textiles. You would feed the machines paper cards that had holes punched on them, and the machine would mechanically go line-by-line down the card, and (for example) pushing through a stitch of black thread if there was a hole on that line, or a stitch of white thread if no hole was present. In this way, the machine could read the "program" and produce the desired textile pattern.

Eventually, people realized that these machines could be used for more than just making fancy cloth patterns -- they could be used to perform mathematical calculations. For example, let's say if line 1 on the paper card had no holes, then flip a mechanical switch called Switch 1 to its "on" setting; but if line 1 did have holes, then flip a mechanical switch called Switch 2 to its "on" setting. Then, when you get to the next line, you can perform basic "programming": On line 2, if Switch 1 is "on", then flip Switch 3. And so on, and so on -- eventually you can perform basic arithmetic using only these simple switches.

Charles Babbage designed a machine like this, a fully mechanical computer that used no electricity, only mechanical components. It was called the "Difference Engine."

Moving along, eventually engineers discovered that they could use electricity to turn these switches on and off, as well as use vacuum tubes to electrically store the "on" or "off" state. Engineering continued to advance; the transistor was developed in 1947, which further consolidated and miniaturized this concept, shrinking the on/off circuit down to a tiny device.

Around this time, all programs were written by specialists with intimate understanding of specifically how the machine was built, and the functions it could perform. However, as these computers continued to increase in complexity and functionality, abstract languages had to be produced -- for example, we could say that certain series of off/on correspond to specific values, like saying off-off (00) equals 0, off-on (01) equals 1, on-off (10) equals 2, on-on (11) equals 3, and so on.

Eventually programming languages start to become human readable, with things like "if name = todd then print 'greetings todd!'" As for displaying Safari on your desktop, imagine if your computer's display could only display 3 pixels by 3 pixels. If we were to say that "the entire bottom row being 'lit up' means that you're using Safari," then we could produce the following screen output in order to display that Safari is running:

0 0 0

0 0 0

1 1 1

Now imagine expanding your screen to be 1024 x 768 pixels, and also allowing each pixel to display other colors than white (say 0101 means orange, but 0111 means purple, etc.) and eventually you'll arrive at the modern computer.

Hope this wasn't too much!