The significant difference is that public nakedness (which isn't specifically illegal in most European countries) and shitting on the curb have concrete consequences for others. The laws are there to protect others from unwanted sexual attention (exhibitionism) and literal disease (shit on the street).
The limit for the freedoms of one person should be the safety and freedom of others. Burning books does not infringe on other's safety or freedom.
Finally: it's stupidly easy to circumvent this. The same provocative assholes that are burning Qurans now, will just shift to other forms of desecration or other ways of offending Muslims. If the goal is to prevent protests that provoke authoritarian or extremistic regimes, you're just going to have to make that the law, because laws like this will just make people protest in another, equally provoking way.