Who was hurt by Reconstruction in 1865 and why?

It is important to know that Reconstruction was a project that was never completed.
The purpose of Reconstruction, which was started in 1865 and was discontinued after Rutherford B. Hayes signed the Compromise of 1877, was not only to rebuild, or reconstruct, the South, but also to provide black people with political agency and property. The promise of "forty acres and a mule" was made during Reconstruction, but was never fulfilled.
Southern whites' resentment of the federal government and of the North may have intensified during this period. Firstly, there was the matter of black people becoming members of Congress. Secondly, federal troops continued to occupy the South. Thirdly, opportunistic northerners, frequently called "carpetbaggers," went south to profit off of the South's diminished status.
Given the historical record, in my view Southern blacks were hurt most -- not by Reconstruction, but by its unfulfilled promise. Hayes's compromise with Southern legislators resulted in the disfranchisement of black people, and in the creation of a new system of bondage: sharecropping. 
In this system, white planters hired black workers to pick cotton or other crops on their land. For a season of work, the workers would receive shelter, a parcel of land on which they could have their own gardens, and a share of the profits from that season's crops. However, very frequently, planters would cheat workers out of their fair share of profits.
In addition, lynchings became very common soon after Reconstruction, as a means of controlling and terrorizing black populations and diminishing their potential political and economic power.