Yes, the "Equal Protection" clause has been used a lot by the courts, just as the "Commerce Clause" has been used by Congress to imply that Congress can pass whatever legislation it wants to as long as it can make a hand-wave to the commerce clause
The position of the various courts these days, seems to be that no government funding of any activity is allowed unless every identifiable group benefits equally from it. Thus you may not fund libraries for people to read in, unless illiterate vagrants are allowed to also use the facility as an informal shelter. Thus you are not allowed to fund public schooling unless each identifiable group comes out with an equal level of educational attainment (which is the point of "No Child Left Behind").
In this legal climate, government funding (especially federal funding) of any activity comes with a huge mass of strings attached.
The only solution, once the system has been made sufficiently unworkable, is to abandon it entirely, as increasing numbers of middle-class parents are doing. Up until now, the upper-middle-class has been able to escape the social pathologies of the underclass by moving deeper and deeper into the suburbs. As soon as that approach becomes no longer workable, you will see increasing middle-class support for radical change
I seriously see NCLB as an attempt to begin that change. I've been really surprised at the number of FReepers who reject attempts to bring accountability to public education.