A transistor is not merely a simple switch. Certainnly it can be used as one, and it is used as a simple switch in computer circuits. Those links only address their use in computer circuits where they are used as switches.
When used in their linear regime, transistors can be used as an amplifier for continuous time signals (analog signals). Your computer speakers, car stereo, home theater, I-Pod would not work if transistors could only be used as simple switches.
The same goes for vacuum tubes. The first computers used vacuum tubes, the same ones used in audio amplifiers. I have a few tube-based flip-flops in my junk collection that use the same 12AX7 dual triodes that are used in my guitar amplifiers.
Here's a page that describes the linear operation of a transistor:
http://fourier.eng.hmc.edu/e84/lectures/ch4/node5.html
The 'input' to the circuit is Vbe, which causes a current Ibe to flow into the base of the transistor. In response, a collector current Ic flows into the collector of the transistor. The magnitude of Ic is related to Ib by the current gain of the transistor beta:
Ic = beta * Ib
Beta is a number larger than 1, and betas of >100 are very common. So for a small amount of input current, we get a large amount of output current through the collector of the transistor. Since we get more out than we put in, we have
amplified our base current, so we're using the transistor as an amplifier, not a switch.
The page goes on to say the transistor can be operated in three regimes:
1. Linear region (what I have just described; the transistor is used as an amplifier)
2. Cutoff region (Vbe is low so there is no base current. Ic is essentially zero so the collector current is 'cut off'. Another way to think about cutoff is that the transistor is switched off.
3. Saturation region: Ib is at or above the value at which collector current no longer increases. We can drive more Ib but Ic will remain at its maximum value. Another way to think about it is the transistor is fully switched on.
When used as a switch, a transistor goes in between saturation and cutoff; fully on or fully off, just like a switch.
The same thing goes for vacuum tubes, FET's, and several other semiconductor devices. SCR's, IGBT's, etc. are exclusively used as semiconductor switches, but those are meant for high power, not for computer circuits. Besides, no one even mentioned IGBT's so why am I even talking about them?