Having lived in the South for all my life except two years, I will say no. But it is Clemson, so you would work fine for you. I will say though if you go for a job interview and someone, whether they be in HR or not, sees it on your 4runner, such may send the wrong signal about yourself to a potential employer, except in a very limited niche market. Yes, it has come to where some employers do take notice of the autos their potential employees drive.
The Confederate flag for me represents a Southern heritage that should be remembered for what it was back in that period of time, and how the South viewed itself then, not for what it is today. I had zero problems with the flag being removed from flying over the SC Statehouse, but do believe it should be kept on State grounds. In Charleston, SC, after the Civil War, no one, except federal bodies of government, flew the Stars and Stripes until 1941, when the US entered WWII.
I don't see nearly as many Confederate flags in Charleston now when visiting my retired folks as when I was in college there in 2000. I attribute such to the droves of people that have arrived from Ohio, Michigan, Penn, and other states. With the influx of these northern interlopers as old timers call them, I expect to see fewer flags in the future there and in the South in general.