Shuttles are any small craft that is able to land on the ground and is designed to dock with orbital ships or stations. Shuttles, specifically, do not have FTL capabilities. So FTL-capable ships that are able to land on the surface or dock in larger craft are not considered shuttles.

There are more specialized varieties of shuttles, such as dropships, fighters, heavy-lift, or commuter shuttles; however, all shuttles more or less function in a similar fashion as described here.

Almost universally, shuttles use a Quantum Capacitor as its primary power source. These are essentially ultra-high density batteries which are enough to power a shuttle for hours or, in some cases, days, without needing to recharge. They are also incredibly safe because they tend to not explode or catch fire very easily; however, when destroyed, they are very disruptive to quantum computers found in many applications and also to FTL travel.

Typically, a shuttle will also have a low-output fission-based reactor as an APU (auxillary power unit). These reactors are not enough to power the shuttle for extended flight, but are enough to power life support and basic functions. They can be used when the shuttle is idle to conserve main power, and to sustain life support in case of emergencies.

These fission reactors are akin to RL labratory reactors and are room-tempurature stable and fully self-contained. In case of a shuttle accident, such a reactor can leak radiation, but in an extremely localized area and be relatively easy to clean up. Even when damaged, they are not typically a hazard to nearby people, though of course you probably don't want to spoon up next to one if it's leaking. They also are reasonably difficult to explode. That said, because of the safety of these reactors, the output is also very low.

Shuttles have multiple systems which enable them to fly. Some of these systems apply only in space, some apply only in atmosphere, and some are used in both. Typically, shuttles will have at least reaction control thrusters (RCS) for space flight, sealable ramjet engines that can be used in space or atmosphere, and gravity manipulation fields for atmospheric stability. Many shuttles will also have Ripple Drives that are not powerful enough to go FTL but can be used for high-speed in-sector travel.

RCS thrusters are used for space flight only. Most shuttles will have RCS thruster packs mounted in the 'corners' of the ship. These thrusters allow the ship to move in all dimensions; generally the more a ship has, the more agile it is in space.

RCS thrusters work by expelling some form of pressurized gas or by ignition. Usually they require some fuel to operate, though the exact fuel may vary from ship to ship, being one of the more annoying aspects of maintaining a large variety of shuttles.

These are generally your 'light touch' engines, used during docking and more careful manuvers.

Shuttles often employ a modified version of a ramjet; the air intake can adjust to to deal with different atmospheric pressures, including completely sealing to turn the ramjet into rocket.

When in atmosphere, these prove to be very fuel efficient and provide the extremely high level of thrust needed by most heavy shuttles. Often they are in engine pods which can be directed for VTOL operations as well as more normal flight.

The exhaust cones are carefully calibrated to try and minimize noise to varying degrees of success. Certainly, you wouldn't want to be right next to one of these without hearing protectors.

In space, they can provide thrust as well; while in space, they require an oxidizer because the air intake seals up. This limits the range of the ramjet, but shuttles that need an extensive range in space will typically use Ripple Drives for that purpose.

One must bear in mind that the majority of shuttles are not sufficiently aerodynamic enough to produce lift on their own; almost universally they cannot glide. There are always exceptions to this; fighter ships may have sufficient wing surface for flight, and some shuttles use a 'lifting body' or 'flying wing' shape to have some aerodynamic capabilities. But the vast majority are more or less flying bricks.

Furhter, it's notable that the manuverability in atmosphere of most of these craft is varying degrees of “not great”. Some notably poor performing ships are military dropships, which are designed to go more or less straight up and down as fast as possible and have very little in-atmosphere manuverability.

How these craft can maintain flight is by use of gravity manipulation. Projectors along the undersdie of a shuttle's hull are used to attract ambient atmosphere particles, thus increasing the density of the air under the shuttle higher than the density above the shuttle, thus producing lift. This lift, combined with the ramjets, is plenty for normal flight operations. When low to the ground, the shuttle's gravity projectors interact with the gravity of the planet below, allowing most shuttles a fairly easy way to hover up to about 50 meters off the ground on this effect.

It is very difficult for a shuttle to crash into the ground; the gravity projectors are a very simple 'apply power, get gravitons' kind of system, so as long as there's some kind of electric power still on the shuttle, the gravity projector can be used to skip the shuttle off the surface and cushion it so it doesn't kill the occupants. It will still be pretty rough and not a great experience.

A full article explaining ripple drives is here and I won't rehash it. Ripple drives are typically used for FTL, but low power ones can be used for moving efficiently at sublight and also to provide some shielding.

Ripple drives cannot be used in-atmosphere as they will negatively interact with the atmospheric particles, in potentially explosive or otherwise catastrophic ways; they are strictly for in-space operation.

Any long range shuttle shuttle is likely to have some form of ripple drive as it is more efficient than ramjets for long distances.

Typically, a shuttle flight will go something like this:

1. Starting on the ground, the gravity projector will be used to ease the shuttle up off the ground and into the air, up to about 50 meters. If the craft needs to taxi, it will hover and flux the gravity projector to creep the craft over the ground or even use its RCS thrusters. More typically, shuttles have engine pods that can rotate and allow the craft to use the ramjets to VTOL. However, some craft have to ascend more like a traditional aircraft after getting off the ground.
2. In atmosphere, the ramjets are used in combination with the gravity projector for flight.
3. As the altitude gets higher, the ramjets start to close up. When the atmosphere is too thin to support flight, the ramjets close up entirely and operate as rockets.
4. In orbit, the ramjets may continue to be used or the ship may use low power ripple drives if equiped.
5. When manuvering to dock, the craft will use its RCS thrusters to align and dock. When landing in a ship, once again the gravity projector comes into play, often in concert iwth the RCS thrusters to nudge it into the correct spot.