I would classify protest in two types.
1st one is protest against film's content & 2nd is protest against the person and his film.
In 1st kind of protest film don't lose much of its business but creates good hype among public for such kind of film. Film may lose few crores in short run but in long run it helps in compensating those loses or even benefitting it. Examples are Haider, PK, My Name Is Khan (Bit of 2nd too), Jodha Akbar, etc.
2nd kind of protest are against individuals and their films like what happened during Dilwale & Fanna. Fanna wasn't released in Gujarat while Dilwale faced such protest in Centeral India.
Thing which go wrong for Dilwale was it faced Protest & Clash. Protest costs it around ₹10-15cr in 1st week but by the time Protest thing cool down Bajirao Mastani did the damage resulting in losing of screens in 2nd week despite pretty good trend in weekdays. This cost Dilwale around ₹20-30cr in 2nd & 3rd Week, if it hadn't loss those 1000 extra screens. So if Dilwale was solo and had faced protest it would have affected it by hardly 5-10cr in Weekend but clash gave exhibitors an option which co-incidentally did really well.