Is it Possible to Limit USB Port Current With a Resistor?
It looks like you are designing so-called "low-power host". In accord with USB 2.0 specifications, Section 7.2.1, such embedded hosts have a right to exist. You can limit ports on this kind of host to 100 mA, it will be formally ok. It will be also OK if your software stack will connect only to certain class of devices, and reject anything else, as long as the list is declared in device specification. But if your device takes power from external power adapter from AC outlet, there is no excuse - all USB ports must hold VBUS for at least 500 mA load.

If you really want a USB-compliant device, there are hi-side power switches with programmable current limit. For example TPS2552D can start from 75 mA and up.

In case of 100 mA limit, your host software stack should implement strict power policy: during enumeration it should check for power requirements, and n ot configure the attached device if it reports higher than 100 mA consumption. It is likely that vast majority of flash drives might be rejected by this policy, but this seems to be your design choice.

As a last resort, you can try to use a resistor to limit power draw, but it will protect your circuitry only from intelligent devices as smartphones. Current VBUS requirements are as low as 4.4V, so if you have +5V internal source, you can put a 6-Ohms resistor in series. So any device within 100 mA power range will see dropping voltage, but all within USB specifications. If a phone is connected, it will reduce its power intake to maintain VBUS above 4.4V. It is likely too low to charge it, so it will drop off. But some devices might ignore this voltage drop, and load your circuit to full 1 A or something. So a resistor would be one ugly hack.

Also, feeding USB port directly from vital system power rail is a dangerous proposition. You will need to somehow de-couple the USB port from system rail, put a sizable low-ESR capacitor (~120 uF), to protect your internals from inrush currents (which could be up to 5 - 8 A spikes) when a device is hot-plugged in.