Yes they can be.
Thunderstorms (Cumulonimbus clouds) contain lightning, hail, extreme turbulence, ice, microbursts and violent winds, all of which can be hazardous to commercial passenger jets. They have caused passenger jets to crash before, and will probably play a part in a crash in the future.
Lightning
Commercial aircraft usually get struck by lightning a few times a year. The damage the aircraft receives from a lightning strike varies. The structure of the aircraft is designed to dissipate the electric charge overboard, but the entry and exit points can cause damage to the aircraft’s skin. It can also potentially interfere with the aircraft’s electrical systems but it rarely causes any significant problems.
Icing
Severe icing is dangerous for commercial aircraft. Ice forming on the aircraft structure increase the weight of the aircraft, which increases the stalling speed. It disrupts the airflow over the wings, which is what is keeping the aircraft airborne. Severe icing should always be avoided.
Hail
Large hail stones found within large thunderstorms can cause structural damage to the aircraft and it’s engines.
Updrafts / Downdrafts (Wind Shear)
These can disrupt the aircrafts flight path and airspeed, potentially causing the aircraft to overspeed (go to fast) or stall (go to slowly).
Microbursts
Microburst is a phenomenon found underneath a Cumulonimbus cloud, where a strong downdraft causes a large change in wind direction over a small area. An aircraft flying through a microburst will likely see a large increase in airspeed followed by a dramatic reduction. If the aircraft is close to it’s landing speed at this point, it’s flying close to it’s stalling speed. Therefore a dramatic reduction in airspeed is very dangerous.
