I don't think that "equal protection" applies because "the people" don't vote for President.
Article II gives the power to the state legislatures on how to determine electors to the Electoral College, therefore there is no "presidential vote" for their to be "equal protection" applied.
Within each state, the legislature of that state determines the method of choosing, so "the people" within each state have equal protection, including no protection at all if their state legislature chooses to let themselves select the electors without a state vote (which is perfectly constitutional under Article II).
Across states, the methods of choosing vary, so it is impossible to claim equal protection against a plenary power of the states to choose their own methods. California cannot claim "equal protection" to force Nebraska or Maine to do away with Congressional district allocation because California chooses to do it another way. By the same reasoning, no state can force another state to not allocate its electoral college votes to the popular vote winner simply because it chooses not to.
As a hypothetical, suppose a state decides to award its electoral college votes by a majority vote of the state legislature. This state therefore has no popular vote at all. What does that do to the National Popular Vote compact if one or more states have no popular vote? Do the compacting states try to force the states with no popular vote to choose a different method that relies on a popular vote? Do we have a case where a state demands for itself the Article II right to choose a method while denying another state that same right?
-PJ
So what is the national popular vote? What is the One could make up all sorts of numbers. Anyway, will be interesting.