Unlike Hitchcock's other films, Marnie isn't really a 'shocker,' but rather a psychological character study, which none of Hitchcock's other films could be classified as. I'd say that this departure from the norm is what initially turned audiences away.
The title character (Hedren) is a quiet, disturbed woman who has a penchant for landing a job and, after some time, vanishing taking her employer's money with her. As the film opens, her latest potential victim is widowed publishing company executive Mark Rutland (Connery). He takes a liking to her and even shares a subtle but memorable kiss with her one evening. True to form, however, Marnie steals money from his safe before disappearing. This moment, curiously, is the only point in the film that suspense is generated, as Marnie must time her actions precisely before a passing custodian sees her.
However, Mark manages to track her down. He was helped by the fact that his friend Sidney Strutt (Martin Gabel) had previously fallen victim to Marnie's tactics & that Strutt introduced her to Mark prior to that (Marnie, naturally, used a different name and a slightly different look at that time).
Here lies the best moment of the film: Mark has tracked Marnie down and has every right to hand her over to the police (I certainly would, no matter how attractive she may be). Instead, he blackmails Marnie into marrying him in hopes of understanding what drives her to do such things.
Once they are married, the rest of the film focuses on the Mark and Marnie facing off. She has a deep distrust of men and a fear of thunderstorms and the color red. Mark initially respects her wishes for privacy on their honeymoon cruise, but (presumably) rapes her shortly afterward when her frigidity proves maddening.
At the same time, Mark does show some kindess to Marnie, such as when he arranges for her to ride her horse, Telepathy (which Marnie is sadly forced to later kill when he breaks his leg). They also try their best to present themselves as an ideal couple, although Mark's sister-in-law Lil Mainwaring (Diane Baker) has her suspicions, fueled by her own love for Mark.
In the end, Mark discovers that Marnie sends the money she steals to her indifferent mother (Louise Latham). He also learns that, as a child, Marnie killed a sailor who was attacking her mother during a thunderstorm. After bringing all that agony out in the open, Marnie wishes to remain with Mark.
Although Hitchcock made four more films after this one, Marnie, in some ways, marked the end of an era. First and foremost, it was the last Hitchcock film with a musical score by Bernard Herrmann. The music Herrmann composed for Vertigo, North By Northwest, and Psycho was magnificent, and the same can be said for the score for Marnie, which may be the most romantic musical score for any film I've ever heard. However, studio pressure eventually led Hitchcock to instruct Herrmann to put a more pop and jazz beat to his music. When Herrmann refused, Hitchcock unilaterally cut off all ties with him during post-production of Hitchcock's next film Torn Curtain (1966). The music for that film was composed by John Addison.
Marnie was also the last Hitchcock film which had the traditional 'Hitchcock blonde' as a leading lady.
I, too, initially thought the film was too slow. But as a character study, it comes off better. Today, I'd be surprised if this film wasn't viewed by students of psychology. It is also, for me, the first great film Sir Sean did once he started drinking vodka martinis shaken not stirred.