Using the Raimi version as an example. Its true that ita not entirely Peters fault that Ben died (hes not the one who shot him, after all), but he does bear some responsibility in the fact that he could have easily stopped the guy who ended up doing it but let him go because he was being petty and wanted to get back at the dude who ripped him off (This is one place where the line With great power comes great responsibility hits home.) Peter didnt heed his uncles words, and one of the results of his failure to do so was the death of his uncle, which both proved that Ben was right and illuminated just how badly Peter had failed. And this is only a small part of all the things that would go into creating a sense of guilt in that scenario.
There's also that he had Ben drive him to a library as a lie to go wrestle instead, and that it's entirely Peters fault that Ben was there in the first place, and on top of that he let the robber get away when he first encountered him.