Most big jet aircraft fly from 30,000 to 40,000 feet above the ground. At this altitude, the air is thinner and the airplane an go faster on less gas. Also, very strong winds this high up can make the airplane go faster.
In the atmosphere, the higher you go, generally the amount of moisture decreases. Take a look at the picture of the atmosphere
Most big jets fly at the top of the layer called the troposphere (higher than Mount Everest!) Since there is so little moisture here, few clouds are able to form.
When there are clouds this high up, they are usually one of two types. The first is cirrus - wispy ice clouds that really don't affect the airplanes. The second is called cumulonimbus - or thunderstorms. Thunderstorms can grow to higher than 50,000 feet! No airplane wants to fly through a thunderstorm.
In big jets, the pilots try and make the flight as smooth as possible. They won't try and fly through thunderstorms (very bumpy!), and since they fly so high, they are above most of the cirrus. A good thin to remember is the higher you fly, the fewer clouds there are.