Many of the Historically Black Colleges and Universities in the South were actually founded during the Reconstruction period in the aftermath of the American Civil War, as part of an effort by the victorious Union, Northern missionaries and activists, the Black community, and Southern Republicans to bring education to the South as a requisite for the establishment of free labor and through that of social, economic and political progress. For example, Northern philanthropists and the Freedmen's Bureau collaborated to found Atlanta, Fisk, Hampton, and Tougaloo, the first colleges in the South that accepted Black students, to form teachers for the equally new public schools that were founded for Black children.
Education for African-Americans in the immediate aftermath of the war was a mix of a sincere desire to help Black people through education and the racist assumption that "slavery had produced a “degraded” people, in dire need of instruction in frugality, temperance, honesty, and the dignity of labor". Again, education was a cornerstone of the Republican free labor ideal, for they believed that only an educated laborer would be able to make the conscious choices that lead one to success: be diligent and good at your work, understand your contracts and negotiate for the best terms possible, and be frugal and smart with the money you earn. An ignorant laborer, by contrast, would be profligate and lazy, unable to achieve upward mobility and likely to turn towards radical means in order to make a living.
Education, in this regard, was both a means of uplifting the freedmen and a "mechanism of social control", that sought to teach this recently liberated people the values, duties and rights a free citizen needed to prosper in a free labor economy. Especially dear to Republican ideology was the conviction that there existed a harmony of interests between workers and capitalists, and that to resort to strikes or pressure the government to create legislation to benefit workers was unacceptable meddling with the laws of political economy that would inevitably lead to social disorder, radicalism and revolution. “Popular education", prominent Republican Carl Schurz declared, "is the true ground upon which the efficiency and the successes of free-labor society grow".
However, the education Republicans envisioned, and indeed the one offered at first by most of the HBCU's, was one of "mechanical pursuits" and "manual education". So, more of an education in the trades, seeking to form mechanics and skilled laborers than lawyers and doctors. Such kinds of education would allow the ambitious and driven African-American youths to become competent laborers, by gaining valuable skills that would allow them to climb the economic leader and achieve respectability and economic independence. The Republican press for example gave hearty support to the "The National Farm-School, for colored orphans and for the children of colored soldiers", an institution that sought to make their pupils into "practical and competent farmer[s]."
Still, and despite their outward support, initiatives for Black education found little direct support from the government. The Freedman's Bureau actually didn't found many schools or colleges itself, instead cooperating with Northern philanthropists and volunteers (most of them women, who saw themselves as a second army coming South to end ignorance after the first male army ended slavery). Bills allowing the Federal government to found schools, or even to give money to the states so that they would do it themselves, failed as Republicans became unwilling to continue pushing the "activist State" forward and instead insisted that African-Americans should carve their path to success without government aid.
Still, and despite everything, Republicans were wholly sincere in their belief that education for African-Americans would lead them to success and independence - and Southerners believed it too, and that's why they opposed Black education so bitterly. During Presidential Reconstruction, when President Johnson basically gave the Southern states, under the control of White people of dubious loyalty, a free hand to make and enforce laws, the States refused to make provisions for Black education, restricting it or making sure it was way inferior to the education offered to White children. And that's saying a lot given that public education in the South had been deplorable, even for White people. Louisiana dismantled the education system established during the war and North Carolina went as far as dismantling its entire public school system, apparently believing it was better for no one to be educated than to allow Black children to get an education too.
The period of Republican rule after the passing of the Reconstruction Acts resulted in a boom for education, as the new Republican regimes, pushed forward by enthusiastic Black legislators, sought to protect and expand education for African-Americans as much as possible. Southern Republicans also tried to "democratize" the institutions of higher learning - most of the HBCUs founded in the aftermath of the war were, like I said earlier, more like trade schools than modern universities, but Southern Republicans also took measures to allow African-Americans access to other already existing institutions of higher learning where formations in science, the humanities or finances could be achieved. For example, the University of South Carolina was forcibly integrated by the State government - a majority of White students and most of the faculty promptly withdrew in protest, but the State, undeterred, brought teachers from the North and abolished tuition charges.
Others were not prepared to take such steps. The University of Arkansas accepted several Black students, but they were taught separately. In Mississippi integration wasn't even attempted, with Alcorn University being explicitly created as a "Black university", so that the State university would remain for White students. In this you can see one of the seeds of HBCUs - creating separate institutions for Black people allowed White people to keep their own institutions. But that laid in the future, for Southern Whites remained bitterly opposed to Black education. Whenever a state was "redeemed", that is, fell under Democratic rule again, the systematic destruction of public education was sure to follow, as White Democrats identified education as a threat to White Supremacy. Again, their racism was so virulent that they didn't mind destroying education for White children too - Louisiana's literacy rate for White people actually decreased, the only state in the Union where that happened. Education was not completely destroyed, certainly, but it was segregated under the principle of "separate but equal". Needless to say, this doctrine was little more than a cruel mockery, for the education, resources and installations offered to Black people were much inferior.
The end of Reconstruction also saw a radical change in the ideology underpinning education, for while Republicans stressed self-reliance and the harmony of economic interests, they also supported equality under the law and, often, Black suffrage and rights. After Redemption came "divorce of schooling from ideals of equal citizenship", as education was advocated for as something Black people should do instead of politics, instead of being part of a larger effort to achieve Black equality. This is known as the "Hampton School", named after the Hampton Institute in Virginia, which flourished under the leadership of Booker T. Washington. But here was a different version of the free labor ideal. Superficially, it remained the same - men could, through education and hard work, improve their social and economic station and achieve respectability; workers and employers shared the same interests, and what benefited one benefited the other, while measures that encouraged class struggle such as strikes were wrong and unthinkable; and "class legislation", that is, government help for one class was unacceptable meddling that only tended towards evil.
The thing is, free labor under those terms only worked if people were truly equal and social mobility was possible, so that it was truly only their efforts that determined their success. Factors such as birth, nationality, race and inequality had to be ignored. When faced with the fact that employers and workers had different interests, that social mobility was not possible for all and that instead a permanent proletariat existed, and that some people needed the help of the State to prosper because of systematic factors, Republicans changed their tune. Now, all people who asked for the government to intervene in the behalf of workers were violent agitators, bloody communists ready to inaugurate revolution and confiscate property because they didn't want to work. Such people were not only foolish, they were dangerous, and that contributed not only to the Republican Party increasingly becoming more conservative and more in favor of big business, but also to the end of Reconstruction, for Northerners came to see governments that included Black people as government controlled by an ignorant proletariat that sought to use the State for their own terrible ends.