I don't think anybody is blaming Atari for putting TTD on sale for money. Heck, I was even planning to buy it until they pulled the obnoxious stunt of removing OpenTTD.
And even that could've been okay if they actually explained what was going on, but it's all very hush hush, which does not instill trust and understanding. If they were transparent about motivations and reasoning, they'd likely catch a lot less flak for what's going on right now.