In the 70s and 80s Manly had a very big cheque book and bought the best players from both Souths and Wests, sometimes to play lower grades. This caused some hatred. The success of the team over the years has caused some of this. The video - Fibros and Silvertails explains some of this.
Another issue is that due to our success, many Manly personalities became involved in the media, in administration and in coaching and selecting at the top level. Some claim that Manly had too much influence in the running of the game and that the team had favourable consideration in terms of scheduling, judiciary, rep selection etc. It was one of the reasons for the Superleague split.
A final reason is that (wronglyl) Manly have been blamed for the demise of Norths who were many peoples second team.
All these factors plus those above contribute to Manly's hated status - though Manly fans don't care. A prominent Manly supporter Vidmar, sells a T-shirt along those lines: Noone Like Us - We Don't Care.
In the 70s there was an old saying: I support two teams every weekend, my own and whoever is playing Manly.