this isn't as big in germany as you might think. The court decision was preliminary, a higher court will deal with this issue within a year, and make a definite ruling on the matter.
I have read up on some stories in the german press, and it is quite clear that the court had a difficult decision to make, balancing the freedom of religion and the separation of church and state, both of which are important parts of our constitution. Personally, I am satisfied with the compromise ( to allow the boy to pray in a separate room, as long as it does not disrupt the school life ).
I would also expect this prayer room to be open to students of all faiths. As long as the school does not force their students to attend religious ceremonies ( such as prayers or masses ) or choses one religion over another, I don't really see a problem. Even if the prayer room was on school property, prayers are only allowed during breaks, and therefore every student's private matter. In other words, as long as prayers or other religious ceremonies are not part of the regular school schedule, separation of church and state is still upheld.
Even if religion is not a big part of my life, I realize that it plays a major role in the lifes of other people, and as a liberal and tolerant person, I respect those peoples' right to have the opportunity to pray to the deity of their choosing at the time when it is appropriate, feasible, and doesn't put someone else at a disadvantage.
The more interesting question to me is, lowing, if a buddhist, or hindu, or jew, or a follower of a different religion other than islam had asked for the right to pray during school, would it even had gotten your attention ?
A lot of high schools here in germany have so-called "rooms of silence" or "rooms of peace", where students may go to to pray, meditate, or do whatever floats their spiritual boat. That is not uncommon.