The nature of the site doesn't change the information it presents. I don't understand how it's reasonable to present an article claiming one such similarities, with no citations on the "important" half of the information, and then reject an article with citations to the reputable source for this information, on the grounds of "trying to combine religion and logic".
The article I presented uses simple logic, mainly that the alleged similarities have no reputable source, and comparison from the Book of the Dead as it relates to the Bible.
The man who started this whole thing is apparently named Gerald Massey, and it seems as though he essentially made the whole thing up. Here's some other sources, and that Stupid Evil Bastard site is definitely not apologetics based if that's your issue.
It's not an atheist doing good that makes him an enemy of God, it's an atheist who has sinned in the past. I'll agree it's scary, though perhaps not in the manner you're thinking of. And yes, there will always be some who think atheists are always evil all the time. However, they are actually fewer than there are made out to be.
Now, as for Jesus existing- I've found a page of recorded quotes, many of them by prominent Roman officials. There's some others too. It is an apologetics page, but the people involved have no input, except summarizing the ending portions of some of the letters they quote from. After some Google searches, I can say that many of these are reliable quotes. Perhaps you'll find differently?