Because the Confederacy virtually defined itself by its slave-based economy and the Union didn't. All states North of the Ohio and north of the Mason-Dixon Line had individually legislated emancipation by 1804. Furthermore, while the Confederacy was frankly proud of its slave economy and went through all sorts of ethical contortions to show that it benefited the slaves, slavery in the Union as whole had grown insidiously and opportunistically. Its only theoretical "justification" was that the Bible didn't condemn it. Despite the nearly universal white racism of the period, Northern state governments were not "proud" of the institution and certainly did not define themselves by it.

When the question came up of extending slavery beyond the Mississippi, the Northern states opposed it but were forced into various compromises.

And of course it was the Union itself that ended slavery by defeating the Confederacy. Which makes up for a lot, even if abolition was not originally a Federal demand.

Chattel slavery is thus a weightier "ingredient" in the Confederate flag than in the U.S. flag. (Not to mention that the current U.S. flag is not identical to the flag of 1776: many more stars for more states, in the majority of which slavery has never existed.)

Of course when you're talking about the "real meaning" of conventional symbols, logic is never a complete guide. See my previous post.