1) If you're using a level based system for characters (not for the crafting levels), you could easily have them level up from crafting the same as fighters would from combat. This would eliminate the scenario where the crafters would be at a disadvantage trying to reach higher level materials in more dangerous areas. Additionally, you could allow crafters to make special, powerful armors and artifacts that would allow them to run right past traps and monsters without taking too much damage, so long as they don't stand around too long and try to fight. After all, there's a difference between "combat" and stumbling through an area, oblivious to the beating you're taking.
2) Have an option of buying the raw materials (either player driven economy or at NPC shops), for the people who just want to make stuff, without the hassle of navigating dangerous areas to track down the components.
3) If crafters are expected to be more financially wealthy than fighters (surely you'd get more for selling fine wares than from picking up stuff off corpses), then you could allow them to hire NPC bodyguards to protect them through dangerous areas. Maybe they could even have an option of hiring NPCs to go gather raw materials for them. This point provides an alternate to each of the above.
4) Finally, I would definitely recommend that you spread the materials out across the world. If you leave them all in one place, not only will players cluster in the beginning areas, but you might as well not build anything else. If it's not going to be explored - why bother?
It's fitting you should respond with suggestions when we spent some time the other evening discussing your crafting system :)
1) I'm not using a level-based system - characters' ability to survive in combat depends on weapon and stance proficiencies and Offense and Defense skills, all of which only improve with use. The deterrent items are not a bad thought, but it's hard to reconcile having something like that in each category of crafting skill.
2) This will definitely exist, but I'd like you to be able to gather anything you want to use rather than requiring you sink part of all profits back into procuring resources.
3) I actually like this idea quite a bit. It has a bit of 2's circular economy, but it's more hands-on and the code already supports characters having multiple instructable minions. I think. I'll have to check that.
4) Well, everything will be explored by the people who want to participate in combat as they'll need higher-level opponents to increase their skills, but I definitely want the various resources to be spread out, as I mentioned originally.
I like the notions of deterrent items and hiring bodyguards, and welcome any more suggestions. It's also true that crafters can devote some of their gained experience into levelling up their invisibility spell or hiding skill, but I don't want it to be necessary for all of them :P