IMO profession bonus is the predisposition for that profession to learn skills in that category, and ranks are the skill itself.
So, as you say, you don't train by "magic", but it is supposed a fighter is trained physically and magician not, and at the same time, is easier for fighter to learn weapons skills, so it has lower DP cost too.
Give a new weapon (not skilled at all) to fighter and magician, it is rare tha the fighter knows better than the magician how to handle it?, it has more experience in how to strike with a weapon, and although is not trained with it, this is an evidence.
More about, it is realistic, so when a scientist begin with a new knowledge, he doesn't begin with a +5 or +10, as he has knowledges that aids him in that new area (maybe maths, physic, as summary profession experience), so if you give a science book to a scientist and to a policeman, surely the scientist can tell you more about the topic in only a week, with no need to wait for long time until many ranks developed.
Maybe the problem is that you see too high the profession bonuses, the solution can be reduce them, RMSS/RMFRP have a fixed +20 for main categories (like weapons for a fighter), that is really lower than the final +60 in RM2. so take a look at them.