The major reason for this is historical. Women have historically been discriminated against both by law and by the private sector. Therefore, any actions that tend to harm women are seen as suspect unless they are shown to have an important state interest.
Civil rights laws today are generally meant to protect groups that have been discriminated against. These do not have to be groups that are a numerical minority. Instead, they are groups that have lacked power and have therefore been subject to discrimination. Since women have been such a group, the argument goes, they should be defined as a protected class.