The thing you have to remember is that more people feel the need to complain on the internet, over the number of people who feel the need to praise on the internet. A high number of complaints does mean a lot of unsatisfied customers; however, the actual complaints, how the situation was handled, and so on, are all up for debate. Why? Simply put, a person who reads a complaint, but has has nothing to gauge it by (other than the review/post), will either believe it without though, or want to see more evidence that the complaint is valid. Almost every well established company you can think of has been labelled as some sort of "scam" or has done something to yield a long list of complaints, regardless of how top notch their service is. Of the ones who stay in "good ratings," a large number of them will simply bend over at the waist for customers to simply avoid official complaints.
To the OP- either buy a product for it's effectiveness, or buy it for customer satisfaction. Kaspersky is definitely one that is much more paranoid about various things, and seems to "flag" a fair number of webpages that are actually harmless. Will that affect you? I can't tell ya.