Was it confusing when Chris Evans was Johnny Storm (Human Torch) in two movies, then became Steve Rogers (Captain America) 4 years later?
No, it wasn't confusing. The FF movies weren't really all that popular and they weren't good. Also, the characters looked and acted completely different.
How about when Ryan Reynolds was Deadpool in 2009 and Green Lantern in 2011?
Not confusing at all. The 2 characters are with different movie houses and different comic companies. Besides, Deadpool was a side character.
People are used to the musical chair casts. Hulk is a different actor in literally every movie. Batman isn't too far off.
It's not that they couldn't handle JGL as Batman. It's that it'd be hard to tell people that JGL is playing Batman, but it's a different Batman than the one he already played.