I think there is (or should be) a big difference between objecting to and criticising a religion/organisation/movement (not sure of the right word, but essentially the suprastructure)... a difference between objecting to that, and displaying hatred or aggression toward the individual human members.
I'm sorry if not articulating myself very well, am very much typing as I'm thinking. But to my mind, religious membership (all varieties) is much more akin to political membership than anything like race. And we can and do criticise people's political leanings all the time, regardless of whether or not we know anything else about that individual.
I own and have read the Qur'an, plus most of the Bible, and a variety of other religious books. If these are to be taken as the 'manifestoes' of their respective religious ideologies, then I find all of them objectionable.
I find them all objectionable because they all advocate prescriptive behaviour and systems of punishment to inflict on other people, not just spiritual/moral guidance for an individual to follow and keep to themselves.
As it is, I think even religion (the suprastructure itself) could be harmless if kept powerless and confined within the agreed laws of the land. But, unfortunately it doesn't work like that... at least not yet.
I object to the religion itself as an ideology, but not the human members who follow it. I object to Islam, but not Muslims. I object to Christianity, but not Christians, Judaism but not Jews, etc etc.
Likewise I object to UKIP but would not expect to be called UKIPophobic, nor would I insult individual members/voters, because they are human and all different. But, like most (?all) religion, the ideology itself I believe contains toxins that outweigh any potential benefits.