When a young man converts to Islam for the love of a girl, he finds his life thrown into chaos when the mentor he befriended ends up being a terrorist, intent on bombing a train -with him omboard.

Inciting incident, clear motivation and goal these are your primary concerns in plot construction and subsequently a logline.

The latest draft of the logline seems to brush over what reads like an inciting incident - finds himself on a train with a bomb, and a goal to disarm the bomb. Why then is half the logline spent describing the back story; girlfriend, fianc?, conversion to Islam etc??

Just focus on the plot, if you can't get the plot to come across clearly in a logline after many many tries then it is a clear indication of a problem in the concept.

On another note if the MC is?able to through himself on top of the bomb and prevent wide spread damage, the bomb couldn't have been powerful enough to truly endanger the other passengers. A bomb powerful enough to destroy a train will easily tear through a human body.

The latest iteration adds a twist to the story line that leaves me puzzled. ?She's been "excommunicated" -- although Islam uses another term with a different connotation than "excommunication" conveys in Christianity. ? And he converts anyway.

Hmm. ?I was more interested in a story where it was a straight line conversion. ?He converts because she will not marry an infidel, nor will her parents give their consent (which in traditional cultures is usually required).

Well, whatever version of the logline and story you end up with, isn't it the case that he's converting to marry her -- that is his initial objective goal? ?If so, then I think that's the way their relationship and his conversion ought to be framed.

Again, his girlfriend and conversion to Islam have no impact on the logline as you state you. While it may be important in the film, it is only adding seemingly unnecessary words to the logline. To me, the only thing even bringing up Islam seems like Muslim=terrorism. Which obviously all Muslims aren't, but you're associating terrorism and Islam in the logline. Of course, you're character turns out to be a hero, but still there is that connection.
As for the plot described in the logline only happening later in the film-what does the beginning include? If it is this man converting to Islam, while I am interested in other cultures and such, I(and many other moviegoers/tv viewers) wouldn't really want watch something about a man becoming a Muslim(I would be content with looking up how this is accomplished or asking someone)
It just seems to me that since this is described as thriller, there isn't much of anything interesting that could hold 30 min of the film. Were it classified as a drama, then perhaps showing and building a relationship between the mentor and MC would suffice, and then lead to the betrayal being that much more impactful to the viewer, but even then 30 or so minutes seems a large chunk of a 2 hour or less film to do this, especially since the logline describes the real action, rather than focusing on the drama of the piece.
My suggestion: After his trusted mentor puts him on a train with a bomb, a young Muslim must disarm it before it kills the passengers.(~23 words)
Just a thought, but there a lot of films/tv shows that feature someone with no training having to defuse a bomb/negotiate hostage taker,etc... But this film has a unique element-the fact that the mentor betrayed the MC. So I think it would interesting to start the film with the bomb part, having the MC live, and then have the bulk of the film be about the MC confronting his mentor and dealing with the betrayal, making the film more emotional.
Just my two cents.

Just did a new rewrite.:
"Determined to please his excommunicated Muslim fiancee, a young man converts to Islam, winds up with a ruthless terrorist as mentor and finds himself in a train with a bomb, he must disarm it before it kills the passengers"

Thanks dpg for the research. What the MC is going to do is to offer his own life to save others. ?When he fails to get rid of the bomb or stop the train because of the panic in the train, he evacuates the passengers into other wagons and ends up alone in a wagon with the bomb. He plans to leave the bomb there and get out, but at the last second, a 4 years old kid runs into the wagon. MC realizes that he can not make it out without the kid getting killed, so he takes the bomb on himself to reduce the impact and as such save the kid and the passengers.

Thanks dpg for taking time to do the research. What the protagonist will do is to save the lives of the passengers by offering his own life. When he fails to get rid of the bomb or stop the train because of the panic that breaks out on the knowledge?of the bomb. The MC takes following actions: he gets the passengers to move into other wagons and ends up alone in one with the bomb. He plans to leave the bomb there but a 4 years old kid runs into the wagon just at the last second. MC realizes he can not make it out without the boy getting killed, so he uses his body to reduce the impact of the bomb to save the boy and of course the rest of the passengers.