Nope, no penalties come from those abilities. At worst they grant you no bonus. In general, abilities you gain do nothing at worst (so it's basically never net negative to gain an ability; at worst you don't use it).
Class Base + Int Modifier (negative or positive) for each level. On first level you get 4x skill points so it's always a good idea to take the highest skill class you plan on taking first (in your case Ranger, Rogue or Scout).
Say, you have 12 Intelligence (+1 Modifier). You take the first level in Ranger; this gives you Ranger Base (6) + Int Modifier (1) points (total 7). And since it's your first level, take 4x this number (28). Next level in Ranger is 7 points. Then take a level in Barbarian, you get Barbarian Base (4) + Int Modifier (1) = 5 points.
Note that subsequent Intelligence increases don't retroactively give you skill points, nor do temporary Int increases (such as magic item "Headband of Intelligence" which gives you +2 bonus to Intelligence). Oh, and Humans get special +1 skill points per level. And again, if you have 8 Int, you get -1 to your skill points (level 1 Ranger with 8 Int would get (6 - 1) * 4 = 20 skill points).
They determine what feats you gain as you advance Ranger-levels. If you only intend on taking 2 levels of Ranger, they don't matter much. But if you are a single-classed Ranger, your chosen combat style determines which bonus feat you gain on level 2, level 6 and level 11.
If you only take 2 levels of Ranger, you basically just pick which bonus feat you want on level 2 from the various options (which include Power Attack in Dragon Magazine Extra Styles list).
Compared to normal Fighter, it gets the unique option of dealing a ton of damage by tackling people to walls. As Fighter otherwise has lots of problems gaining any unique options, this is well-liked. If you're not interested on being a Kool-Aid Man tho, it's not the way to go.
It also requires 6 levels of Fighter to fully gain the benefits. Fighter doesn't get a lot of skills or interesting class features so this is kind of a downer.