Are there Islamic militants who are not anti-Semitic (in this case meaning anti-Jewish)? Are there any factions who are militantly Islamic, even to the point of being terrorists, but not considering Jewish people or Israel as their enemy?
In the Middle East context, probably not on both counts (Jews and the state of Israel).
But most Muslims don’t live in the Middle East, and don’t ever encounter Jews, and aren’t close enough to Israel for any military concern. I imagine they have a very negative stance on Israel, but then most of the rest of the world does regardless of whether they are Muslim or terrorist. And of course in the ME the State of Israel is of course a real enemy for Islamic terror groups, which isn’t helping their anti-Jewish hysteria any.
Once you get to the South and SE Asia extremist Muslim groups, most attacks are against other Muslims for not meeting their extremist take on Islam (come to think of it this also applies to a lot of Mid East attacks), with the remainder against Hindus, Christians, etc. I imagine if you talked to MILF members (no, NOT that MILF! 
, the Phillipine one) they might not have a very clear idea as to what a Jew is. Remember these are often poorly educated, often rural young people with limited experience with other cultures. I imagine in Indonesia the venom is against Hindus (Bali) and small animist minorities when not against politicians seen as being poor examples of Muslims.
There are plenty of non-radical Muslims who don’t mind Jews, but you’d have a hard time finding ones who had a positive view of Israel.