How do you usually interpret "egregious"?

egregious has a negative connotation, and is usually used to connote severe examples of evil or wrongdoing. A look at it's synonyms should give you a flavor of the word.

egre·gious adjective: very bad and easily noticed (archaic: distinguished); conspicuous; especially: conspicuously bad, flagrant:

egregious padding of the evidence — Christopher Hitchens>

...the public perception is that too many corporate executives have committed egregious breaches of trust by cooking the books, shading the truth, and enriching themselves with huge stock-option profits while shareholders suffered breathtaking losses. —John A. Byrne et al., Business Week, 6 May 2002

Synonyms: blatant, conspicuous, flagrant, glaring, gross, obvious, patent, pronounced, rank, striking.

Who is a blatantly respected scientist?

I'm perfectly well aware that today the word is (almost?) always used negatively. But even now I can't avoid thinking that usage is very slightly "odd", because when I first came across it 40-50 years ago, it usually had positive associations.

That's not because most actual usages of the word back in the 60s had positive associations. Thanks to the wonders of Google NGrams, I now see how this situation came about...

When interpreting that chart, bear in mind that a significant proportion of the instances before the 80s probably aren't actual "usages" at all (many of them will simply be citing earlier texts). My personal perception, which accords with the chart, is that egregious had largely fallen into disuse until it caught on again in the 80s, at which time only the negative sense was "resuscitated".

In short, I first knew the word with its positive associations because I only encountered it in Victorian or older texts. That wouldn't apply to younger speakers, so they won't see anything odd about the current usage (just as nobody today seriously thinks of terrific as inducing terror).