The Color Structure is actually part of the System.Drawing namespace in the framework. It is used for things other than merely HTML color, including graphics and imagery, where an alpha channel makes sense.
When you're dealing with HTML color, you can just use the FromArgb overload that only specifies red, green, and blue (and alpha to fully opaque).
I think your confusion lies here:
"Since the purpose of Color structure is to specify a html supported color"
That is not the purpose of the Color structure, but rather one specific use of the Color structure. This structure has many other, very valid uses, where having an Alpha channel makes sense. Instead of requiring people to work with multiple Color structures, the framework uses a single, general purpose structure. I believe this was a good choice, since it simplifies the number of types, and keeps the "color" interoperable with other code using Color types.