There was a time in quite recent history when the term Sovietophobia was widely used to target people who opposed communism. However, at the moment it is very hard to find people who would think that communism should not have been opposed at all. Terms like Sovietophobia and Islamophobia are handy tools in branding the opponents of an ideology. It can be used so that it would seem that all critics of an ideology are driven only by prejudice and bigotry.
Things are made much more complicated by the fact that among the current public critics of Islam there really are people who are even extremely xenophobic and racist. These people all too often use the exploration of the very real negative aspects of Islam as weapons in the furthering of their distasteful and anti-humanist agenda.
So, there is really also racist Islamophobia in existence. Most of all the very real fear of Islam is used also to foster fear of immigration and foreigners in general. However, even if there does exist people who criticize an ideology for bad or distasteful reasons cannot stop all critique of that ideology.
The existence of these racist groups makes it all more difficult to make intellectual critique of Islam as an ideology. It is all too easy to lump together this critique of an ideology with those with the racist agenda. Getting rid of that stigma can be extremely difficult, even if one's own version of the critique has nothing to do with racism or xenophobia.
On the other hand, opposing Islam did for a long time mean putting oneself the same side with the likes of Bush regime in the United States after the start of the wars in Afghanistan and Iraq.
However, it should be good to remember that the fact that a state with a distasteful foreign policy is opposing an ideology should not prevent other people from opposing that same dangerous ideology for quite different reasons. One should remember that also opposing communism as an ideology did not mean that one would have in any way despised and hated the people who were forced to live under the communist rule.
It did mean only criticizing of the ideology that had for historic reasons taken power in their home countries.
With religions, it is even more easily forgotten that criticizing a religion as a ideology is a quite different thing than criticizing the people who just happen to live under its rule. They mostly have never had possibility to choose their religion. What is the dominant religion in a givern area is simply a result od many kinds of historical processes and even coincidences.
The fact is that what is the current ruling religion in a given area has mostly been simply decided in the forgotten battlefields of history. Religion is not a genetic property of humans. Even Islam is not genetically inherited; it is no more inherited in birth than communism ever was. Of course, this fact is shrouded from view by the fact that in practice religion is mostly learned in a very early childhood from the family and relatives.
However, in the end Islam is just the same kind of human ideology as communism was. One should be able to evaluate it in a quite similar manner as communism was. Freethinkers and atheist are sadly all too often the only groups in a society that do expect all ideologies to be treated in a similar way. Religious ideologies are mostly given a special status, where they cannot in practice be criticized at all.
Unfortunately, all the fundamentalist versions of Islam just are at the moment a very real threat for the freedom of expression throughout the world. The followers of that ideology have clearly shown that they are ready even violently silence the critique that comes even outside their own ranks.
The freedom of thought is always under severe threat if a mere written or spoken critique of any ideology causes physical danger to any member of a society. If this physical threat leads to a situation where there is not possible critically evaluate this ideology, the freedom of speech is not merely under a threat, but has been lost altogether.
(This piece was completely rewritten on 12th of May, 2012)