She's just saying that it didn't sell well and people weren't here for it which is true, no matter how good the album was or how much she liked it. I'm sure she still likes it, it's just that the songs don't fit her tours, they only fit the Re-Invention Tour because it supported the album and it was very political like the album. The MDNA Tour is the only "political" tour she's done since then, and she did include Nobody Knows Me on it as a video interlude.
