Well depending where the sun is there is more or less atmosphere for light to travel through. This is why the sky changes colour at night. If you have a red sky the clouds are being illuminated by red light, so seen as red in colour.
Clouds at different heights also scatter light in different ways and the density of the cloud makes a difference. So more dence the darker the cloud as less light passes through them.
All of these things contribute to the colour of clouds. There is a good website below that will give you an in depth explanation of this.
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