First off, from the sound of your concept, it's wearing its theme on its sleeve and almost literally waving a flag. Are you not worried that it's just going to read like a manifesto that you're smacking a reader around the head with? Hopefully you're also simultaneously representing some good elements of religion (good deeds/great works done in its name, positive contributions to culture/philosophy/etc?) rather than just writing a thousand-page treatise on why "religion is always bad, mmkay?" (Note: I'm an atheist - I'm not saying this because I don't like you picking on religion, just that if your entire novel is overtly hammering home the same point over and over and over, nobody's going to be interested in reading more than a few pages.) Second, the response to the actual question. Look at some famous revolts and movements, and ask yourself why they chose their symbology. Why have this resistance sprung up? Is the religion they're now fighting an invading one that's reasonably new (i.e. the resistance are defending their own way of life), or is it an old, ingrained one that's been there for some time that this particular faction is attempting to abolish? "Resistance" sounds like the former, in which case you might pick a symbol of the "old" way of life which the new religion is trying to wipe out - so if the religious rules forbid agricultural technology, for example, your resistance may well take inspiration from symbols of technology; cog wheels, spanners, various types of workwear. If the religion outlaws the eating of certain types of foods, else particular activities, symbols and paraphenalia connected with them may also serve. In the case of the latter, is there a particular point or event which led to many joining the cause? If the church publicly executed a famed and popular astronomer for his supposed heresy in pointing out that the world orbits the sun, then your movement may well march under a sun banner, or commemorate certain events in phrases, sayings and battle cries ("Remember the Alamo").
Depends on what your rebels stand for. Look to history for good symbols, look to myth. For my "evil" faction I took a page from the Nazi's who took a symbol of goodness and turned it on its head. For them I gave them a peace symbol with wings. For my "rebels" since they want to fix the (mostly destroyed) world and bring better ways of living (technology, medicine, etc) I reached into Ancient Greece for the story of Prometheus and gave them a symbol for that (A raven in front of a mountain). But again that is just me. I love history and folklore so it fits and fits with my world as well.
Martyred people are frequently featured in resistance motifs in fiction, someone who sacrificed themselves. Their faces on posters with the word "RESIST" underneath plastered all over the walls of a city. If you choose to go down that route, an item or article of clothing they wore could be chosen, like a red scarf or bandanna. But icons themselves, they could be based on anything - a town that was destroyed, a flag of a country or state long gone. Alternatively if you wish to use the opposing forces symbol, you can invert it from the middle out. Let me see if I can do so for you.
