Suppose I'm playing a character with Craft as a class skill. I put 1 rank in it, select Weaponsmith to fit my background and end up with Craft (Weapons) +4. Now, if I later decide I want to be able to make bows and arrows, do I also get another +3 bonus on Craft (Bows) when I invest a new rank? There are different kinds of craft, just like there are different kinds of knowledge, but the class skill bonus for craft is completely unspecified.
Craft is actually a number of separate skills. So if you have the class bonus for craft you have it for all the skills in the craft "family".
Although it is really not clear from the PFSRD entry "Craft is actually a number of separate skills", it doesn't make any sense in real life. As always, if the rules are unclear, we should reach for what makes sense, and the idea that one could be equally efficient in making anything (any craft skill), as long as he/she spends equal amount of time practicing that craft (skill ranks), and being really good at it (+3 bonus) simply doesn't.
The description of what a class skill actually is is:
In addition, each class has a number of favored skills, called class skills. It is easier for your character to become more proficient in these skills, as they represent part of his professional training and constant practice. You gain a +3 bonus on all class skills that you put ranks into.
The fact that each class has only some skills as class skills implies (and reality supports that fact) that there is a limited number of fields one can excel in after completing some form of training or acquiring a certain amount of knowledge, i.e. after gaining a level. Just as it is limited in terms of the number of "standard" class skills (Acrobatics, Appraise, Bluff, etc.), it is also limited in terms of the number of specific Craft skills a character can have as class skills when gaining a level.
So, along with the specific training you completed in order to gain a class level, you could have invested some of your time (skill ranks) in a certain Craft skill. Now, if you gained a +3 bonus for each and every Craft skill you ever had a try at, the rate at which you learned them would be exceptional, which is really not realistic.
Of course, those with more skill ranks could invest more in various Craft skills, and be very good in many of them, but that would be a result of the time and effort invested in gaining a certain skill set, not the result of your character finding it easy to craft something because the basic knowledge of doing that was already covered in his training.
Now, one could argue that, for example, all fighters pretty much fight all the time, swinging their mighty weapons and relying on their hard armor, so they are very experienced with both weapons and armor, have seen many of them in creation and experimented with even more, so they should be entitled to both Craft (weapons) and Craft (armor) as class skills. Well, this could be the case, but not necessarily the default case - I believe that a character having only one such "field of interest" or "field of expertise" (interpreted as having a hobby or being proficient in something) was meant to be the default setting, but one could still gain multiple Craft skills by acquiring certain feats, traits, class features and like (analogously to improving many other abilities in the Pathfinder universe). For example, the Talented Blacksmith trait is one such improvement. The "it becomes a class skill for you" part would be useless if any Craft skill was already a characters class skill.