bad user interface, you have to format all your music to their format to put your music on to the player and/or their products, the music was up to recently DRMed, they limited the content to certain areas, its not always their choice, obscene prices, the few times i actually managed to find the album or song i wanted, another reason why people dislike it, the price was higher than on most competing sites, the recommendation system is complete garbage, despite 95% of the music i have on itunes is metal it keeps recommending the top 5 pop albums of this week, so apparently its based on sales instead of what genre music i listen to, when you download a update it forces quicktime on you, the constant updates i swear theres a new one each time i log on, when you plug your ipod into another computer that has itunes on it itunes will ask if it can delete all your songs instead of asking you if you want to play them, adding movies and music can be complicated for the average user and it abuses this to make you buy your music collection all over, but at a higher price and from them.
im sure there are other good reasons but those are the ones i have run into during my somewhat limited time spent with the program.