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[If the ship was disrupting inertial forces, it would aso have to be disrupting spacetime simultaneously to decouple inertial reference from accelleration. Eg, the ship moves from
frame dragging, and warp drive. This allows the ship to move without inertial and accelleration effects, by moving a chunk of reality around instead of the ship itself. (Further reading:
alcubierre warp drive) Engaging this in atmosphere would be 'bad mkay', because the warp drive creates a sort of event horizon around the ship, and mass-energy from atmospheric particles hitting the horizon would cause them to "stick" to the horizon, building up a huge mass energy wave as long as the field was active. This would reach "OMG! Were all gonna die!" Levels in under a second. As soon as the field was shut off, the energy would blast off like an atomic bomb. Clearly, you can see why this would be a "bad thing." Even in otherwise total vaccuum, the alcubierre metric's tensor field would interact with quantum
vacuum fluctuations, and as such would relase copious amounts of
hawking radiation, and drain the field generator's power vampirically. This exposure to vacuum particle energy would similarly build up on the horizon while active, but would be considerably less intense than atmospheric activation. It would pose a problem for sustained operations, however. Not that it matters too much though, the ship could travel at nearly limitless velocity. Sustained cruises would be a silly idea with a ship that gets to the destination almost instantly.
The point here is that inertial dampening, (decoupling the frame dragging of a masssive object, so that relativistic effects stop happening, or reducing an objects mass directly) in an atmospheric environment would be dangerous in the "epically bad" kind of fashion.
Its possible that your theoretical ship uses concentrated disruption of the
higgs field to alter the ships mass, so that inertial forces are reduced, but that field effect would also effect atmosphere around the ship, and the dirt under it, and the
brownian motion of the raw atoms inside the ship would also be likewise altered. It would tend to make the ship explode. (All matter not at absolute zero temperature is in motion, and bouncing around against each other, tethered in place with electrical forces from the atoms' electron clouds and neuclei. Reducing the inertial rest mass of the atom increases velocity. This is also true of the brownian motion of the component atoms. The effect is that the atoms speed up accordingly to the reduction of their rest mass, as the innate energy of their motion has not changed. This causes a sudden and intense change in apparent temperature of the material, and a precipitous drop of its
specific heat. If the ship was sufficiently hot (say... room temp...), and you reduced its inertial mass 50%, its temperature would double explosively.
If you slowly spooled up the inertial damper so that the heating effect held pace with
blackbody photon emissions, you would be relatively safe....except that your biological activities would suddenly be working with the same chemical energy as before, but now with radically easier to move atoms, and as such, your metabolism would induce spontaneous combustion. If we assumed that our ship is unmaned, or that the crew is in cryo, then we have another problem. Sure, slowly spooling up the inertial damper to allow the ship to cool safely keeps it from blowing up, but now you have to slowly spool it back down again, or the ship will be an superchilled cryonic popcicle when the field is switched off. (All the thermal energy bled out during the slow spool up!)
Long story short: inertial dampers aren't toys. Don't use in atmospheric conditions. Higgs field manipulation has dangerous side effects, use with caution. Don't ignore the safetys on an FTL or ID capable ship.
This concludes this geeky PSA]
[This post edited repeatedly for !!SCIENCE!!]
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