The ITA rankings value good wins and do not put much weight (relatively) into losses. That is by design, to encourage teams to schedule good opponents. If you weight losses heavily, then teams have an incentive to make weak schedules. That system has existed in various NCAA sports over the years, and then we fans complain about teams trying to game the system by refusing to play anyone. Perhaps there is some middle ground, but it is hard for the ITA to find the right balance.
Remember that the initial computer rankings are based on the final poll ratings. Everyone complains about the polls in tennis, also. You have to start somewhere, and the final polls are the only reasonable choice. So, perhaps the SEC was given too much credit in the polls. But then again, outside of the SEC, it seems that there are not a lot of really good teams other than the best five (UVa and Duke from ACC, USC and UCLA from PAC-12, Ohio State from Big 10). The handful of other good non-SEC teams (Baylor, Texas, Oklahoma, Pepperdine, Cal, Tulsa, Notre Dame .... I am running out of names here) are probably not any better than Texas A&M, Vanderbilt, et al. There is a drop-off after Duke and Cal and Texas in their conferences.