Okay, lets look at that claim.
Uncharted begins on a boat, he is 'jumped' by people shooting at him, he claims this has happened before, even if he's lying to comfort the woman, he could decide to bail on the whole thing once they escape that situation, he knows carrying on will likely result in him having to kill more people, but he does it.
Uncharted 2 begins (chronologically, the game actually begins in medias res) with Drake meeting an old friend and deciding to rob something and not hurt anyone, they're going to use stealth and no guns (ultimately they use tranq darts). Drake is double crossed, caught and goes to prison. When he gets out he could have gone back to the States, instead he decides to go along with a plan that they must have known would involve killing tons of people.
It's not a good excuse to say Drake is in a bad situation, because he deliberately puts himself in those situations, repeatedly. It's also not a good excuse to say 'shooting things in games is fun' or 'shooters sell'. Those things are true, but that doesn't nullify the dissonance some people are experiencing. It was touched on why Uncharted is usually the example given, and ultimately it's because it's the worst offender of this by a country mile while still being a major series. Lots of people addressed this in various ways, make the protagonist a scum bag, make the bag guys robots or aliens or zombies, etc. ND have decide to just ignore the issue, and hope people don't care, and for the most part they're right. Uncharted is a massive IP, the second game got huge critical acclaim and Uncharted 3 is going to sell five million copies within the next year. None of that means the debate is invalid.