That's part of it; and then the rest of the components are due to real-world issues, such as the current limiting you mention.
For instance, if you were to look at a schematic for an audio power amplifier, you'd find that about a third of the circuitry (or less!) is related to amplifying an audio signal, and the rest is related to making sure that there isn't a "pop" when you turn the amp on, that the speakers don't get fried if something inside the amp dies, that the amp doesn't get fried if the speaker terminals are shorted, that the amp does something graceful if it overheats, and so on. Practical experience, and looking at a lot of schematics, is about the only way to find out about all those "real-world" factors.
Logic inputs are high impedance - that is, they behave as if they have big resistors in series already. You do not need to add any more resistance.
Logic outputs are low impedance. If for some reason you tied a logic output directly to ground, and the output was trying to be high, a lot of current would flow and the IC would be destroyed.
Start with "Art of Electronics", 2nd Ed., by Horowitz and Hill. It is a very good blend of basic theory and real-world practical issues.
Also, read the application notes that the chip makers provide. Many times if you read the datasheet for a part, it will give you sample circuits.