Should one use resistors to protect an mbed when using it to simulate keyboard key presses

It limits current to protect the switch (transistor, etc.) and allows signal sources with limited driving capability to change that node's voltage. Rails generally have high drive capability, or low resistance. Think voltage divider, including source impedance of signal and rail, then let the rail impedance be 0-ohms for simplicity.

Other factors, other than operating current and voltage drops, to determine the pull resistance is charge time and substrate leakage. A 2M-ohm pull-down resistor on a top layer exposed to humidity and salts won't do anything due to sub-1M-ohm electrical resistance of grime layer.

The answer depends on what you want the "default" configuration to be. For example, say you have a down-stream N-channel MOSFET, and you want it default off. Then you would use a pull-down resistor to ensure this behavior if the input becomes high impedance.

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On the other hand, suppose you have an upstream P-channel MOSFET, and want it default off. This time a pull up resistor is required to create this behavior.

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There's also the alternative case where you want a device to be default-on, in which case the above two cases would be reversed (pull-up for the N-channel MOSFET, pull-down for the P-channel MOSFET).

A few other considerations:

1. I2C lines specify pull-up resistors because devices are "expected" to have an open-drain to ground, and thus need some way to raise the line potential.

2. Analog comparators are usually configured as open-drain devices, and thus also need pull up resistors to get a high potential output.

3. You may draw more current using pullup/pulldown resistors, depending on what's hooked to the input/output.

4. Either configuration could works equally well in your application (i.e. there's no significant advantage one way or the other).

... And any number of very application-specific reasons why one configuration may be preferred.