It is about maintaining the balance of power in the United States Senate. The Senate, because of the two Senators per state format, is the only branch of the United States Government where the Southern States could block being steamrolled by legislation directed by the more populas northern States.
Because the House was determined by Population, (the States of Ohio, Pennsylvania and New York having as many repersentatives as all 11 of the Confederates States) there was no possibility of blocking unfavorable legislation in that body.