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"How would a system like the S-300 shoot down Tomahawk cruise missiles flying at below 300 feet above the ground?"

Perhaps by being on an elevation and using Doppler radar to detect the moving cruise missiles? I hope we have a nice big stock of the stealthy cruise variants.

Here's a description of the system under discussion here (not the S-300):

The TOR-M1 surface-to-air missile system is a mobile, integrated air defense system, designed for operation at medium-, low- and very low –altitudes, against fixed/rotary wing aircraft, UAVs, guided missiles and precision weapon. The system is capable of operating in an intensive aerial jamming environment. The system is comprised of a number of missile Transporter Launcher Vehicle (TLV). A Russian air defense Tor battalion consists of 3 - 5 companies, each equipped with four TLVs. Each TLV is equipped with 8 ready to launch missiles, associating radars, fire control systems and a battery command post. The combat vehicle can operate autonomously, firing from stationary positions or on the move. Set-up time is rated at 3 minutes and typical reaction time, from target detection to missile launch is 5-8 seconds. Reaction time could range from 3.4 seconds for stationary positions to 10 seconds while on the move. Each fire unit can engage and launch missiles against two separate targets.
Tor M1 missile launched from the vertical container/launcher. The missile uses cold launch to exit and clear the launcher, and the rocket motor and thrusters are ignited at an altitude of 20 meters.Tor M1 can detect and track up to 48 targets (minimum radar cross section of 0.1 square meter) at a maximum range of 25 km, and engage two of them simultaneously, at a speed of up to 700 m/sec, and at a distance of 1 to 12 km. The system's high lethality (aircraft kill probability of 0.92-0.95) is maintained at altitude of 10 – 6,000 m'. The vertically launched, single-stage solid rocket propelled missile is capable of maneuvering at loads up to 30gs. It is equipped with a 15kg high-explosive fragmentation warhead activated by a proximity fuse. The system is offered as fully integrated tracked combat vehicle, or as a modular combat unit (TOR-M1T) comprising a truck mounted mobile control module and launcher/antenna units, carried on a trailer. Other configuration include separated towed systems, as well as shelter-based systems, for the protection of fixed sites.

Sounds quite formidable, one hopes we have appropriate countermeasures. I'm sure it'd be better if Iran didn't have these...