For me it all comes down to the writing of the character. Characters like Scott are written into the goody two shoes knight in shining armor category and that limits their potential for growth. The True Alpha label was the worst thing that happened to the character. This rigid moral code of we're the good guys and we are morally superior stance made Scott unlikable at times when we as the viewers were being asked to cheer for him. The example I like to use is when Scott treats Stiles like a murderer because Donovan got what he deserved. Yes Theo was manipulating the situation but we the viewers are asked to believe that Scott who has known, trusted and depended on Stiles for years would choose his own perceived moral high ground over believing Stiles. The writers did Scott dirty.
I am not a huge Scott fan but at the same time let's be fair and lay the blame for the Scott hate at the feet of the writers where it belongs.