Wal mart has made manufacturers censor their products or they don't carry them. I doubt these core rule books are going to be altered, but Wal Mart wouldn't normally carry the Book of Vile Darkness or products like that.
This is the long-term threat that Wal-Mart represents. They have a huge amount of pull with any corporation that hopes to sell through their channel -- look at the shrinking of video game boxes over the last year or two as an example. Did any of the manufacturers push for half-sized boxes? No, it's all Wal-Mart and their interest in shelf space.
Would you like to see little, tiny D&D books? Don't laugh, if Wal-Mart got to choose that's what you'd be buying. And, as Najo mentioned, if you'd ever like to see anything edgy like BoVD you can forget that too. You can also forget anyone like Green Ronin or Necromancer who can't sell through lots of 10,000 units every couple months.
Of course, your FLGS isn't going to collapse suddenly because some people buy their 3.5E at Wal-Mart. But it's something to keep in mind. If your FLGS is doing anything for you (stocking lesser d20 titles, stocking minis, giving you a place to play) then you have a vested interest in their health. Do something to support them.
If you dont care if those stores die (and you may not), then consider giving someplace connected with ENWorld a try; Talon has offered a big discount and (I think?) so had RPGNow. If you are glad that the word "Devil" is back after the 2E censorship fiasco you might want to consider supporting someone who isn't going to be pressuring Hasbro to go back to "Tanar'ri".
And if none of this applies to you, by all means, buy from Wal-Mart, et al. They're very good at what they do - which is offer a rock-bottom price.