Basically, when you take a penalty it applies to all attacks which includes all forms of attack rolls such as natural attacks, weapon attacks, ranged attacks, spell touch attacks etc
For example, if you fall prone you take a -4 to your attacks. This term 'attack' gets thrown around a lot and it includes pretty much every single d20 roll you make against an enemy when you try to hit their Armour Class (AC), their Touch AC or their Combat Maneuver Defence (CMD)
Reading the Armour Check Penalty rules
Nonproficient with Armor Worn: A character who wears armor and/or uses a shield with which he is not proficient takes the armor's (and/or shield's) armor check penalty on attack rolls as well as on all Dex- and Str-based ability and skill checks. The penalty for non-proficiency with armor stacks with the penalty for shields.
So if you wear a chain shirt you'd be getting a -2 penalty. If you pick up the feat Light Armour Proficiency then you avoid this penalty.
Alternatively, the highest armour you can wear without suffering a penalty is Leather. Check out the table to see what armour you might be able to benefit from.
Press Ctrl+F and search for "Table: Armor and Shields"