1) Yes, the flag people generally associate with the Confederacy is not one of the several flags that formally represented the CSA, but it is the longest lasting flag of the CSA, formed the key design element of several official CSA flags, was was adopted by the terror groups that formed after the fall of the Confederacy. It is the flag of the Confederacy, official or not.
2) Every flag is a symbol of the nation that flies it, and the flag represents the values and purposes the country adopts. The Confederacy was founded on several principles: State's Rights (to allow slavery), against taxes (on slaves) and individual freedom (of select people to own other people). Whereas the USA was founded on the principle that "All men are created equal", the CSA was founded expressly on the idea that some men were superior, and others subhuman.
From South Carolina's Articles of Secession:
"But an increasing hostility on the part of the non-slaveholding States to the institution of slavery, has led to a disregard of their obligations
they have denounced as sinful the institution of slavery
They have encouraged and assisted thousands of our slaves to leave their homes
A geographical line has been drawn across the Union, and all the States north of that line have united in the election of a man to the high office of President of the United States, whose opinions and purposes are hostile to slavery. He is to be entrusted with the administration of the common Government, because he has declared that that "Government cannot endure permanently half slave, half free," and that the public mind must rest in the belief that slavery is in the course of ultimate extinction."
Not only did that flag represent slavery, but slavery defined and justified by vicious racism. It represents a nation founded on the idea that some people (blacks) are subhuman and exist for the benefit of others (whites). It was founded on the idea that some people are inherently inferior, that the smartest, wisest, most successful black man is inferior to the lowest, dumbest, most foolish white man.
3) Honoring that flag and the symbols of the Confederacy honors the causes and actions of the CSA. Placing the flag and statues of Confederate leadership in positions of honor not only honors people who fought for slavery and racism, but honors slavery and racism themselves. It honors the men who betrayed their country, not as a result of their country's tyranny, but in an attempt to establish a tyranny of their own.
This was an evil cause. The individual honor and courage of the fighters for the Confederacy is not relevant. A hero is honorable and courageous in the service of good and noble cause, while an honorable man in service of evil is simply an honorable villain, and no villain is deserving of veneration. What does that say about the society that honors them? We condemn Palestinians and Muslims who honor terrorists, yet place statues of men who fought for similar goals in positions of honor.
4) The attacker of the church in Charleston was directed inspired by the racist nations of Rhodesia, South Africa (explicitly under Apartheid) and the Confederacy. The attack was expressly racist in design and intent. The shooter openly expressed white supremacist and anti-black racism. There is no doubt that the attack was racist.
5) The flag itself has never represented honorable agendas. It first flew in defense of slavery and racism as a battle flag (and later part of official CSA flags), and was adopted by the Ku Klux Klan as an official emblem as a symbol of racism. After the first Klan collapsed, the flag languished as a generic symbol of "Southern Pride" until the Civil Rights Movement, where it was flown again as a symbol of racism and segregation. The flag, and all of the symbols of the Confederacy, deserve no respect or veneration, but condemnation of the evil they represent.
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Additionally, I need some help. I've been invited and granted status as a delegate to the Young Republicans National Federation this year in Chicago, at the end of this month. As of now, lodgings are covered, I just need to get there. You can help cover the expenses of travel by donating through Patreon or Paypal (at firstname.lastname@example.org). If you've enjoyed my previous reporting on the Young Republicans, you should consider helping. I'd also like to acquire a directional (shotgun) mic before I go, as I may not be permitted to connect directly to the speaker system. (It will also help in my video production generally.)
Finally, if you are in the Baltimore area and need some video production work, I am now taking clients for commercial work. Just email me.