Usually, but not always, the sun is covered by the rain clouds.

A thunderstorm is a storm with both thunder and lightning, and sometimes strong, gusty winds and heavy rain or even hail.

The storm might form  one single cloud called a cumulo-nimbus cloud.  Or there might be a line or clister several thunderstoems together which can cover over 50miles.

So, it isn't surprising that you can't usually see the sun during a thunderstorm - until it's all over!