It is harsh, but it's meant to indicate the difference between normal classes (earned by experience) and Hero levels, which are more like the Level Adjustment of a powerful race-- they're designed to give special powers, which is why the class also has minimum BAB and saves.
Also, if it's 0 + Int mod, it means that the class automatically gets the minimum 1 skill point per level.
Remember, there's the option to take 2 skill points for one Hero point, and if your first level is a Hero level, you get to count your first non-Hero level as your first level for the purposes of quadrupled skill points. Also, since there's no class skill list for Hero, it's safe to assume they can spend those two skill points per Hero point on any skills they want.
edit: If you want to soften that a little bit, you could always make a house rule that your human bonus skill and your INT modifier apply to skills you buy with Hero points, so if you spend one Hero point on skills, you get 2 + Int Mod, and can then spend more Hero points to get more skill points, like the more skilled classes do.