There is no issue at all with using cotton pads while you have your period.
However, when a woman is not niddah, in order to avoid becoming niddah from any staining, she should wear colored underwear (or possibly pantiliners that are not susceptible to tum'ah; please read our article on staining for further details.) The article about feminine hygiene products deals with the question of whether stains found on a pantiliner would render one niddah.
One of the factors that allow us to disregard stains found on pantiliners is that pads are made from synthetic materials and thus are not susceptible to tum'ah. It is questionable whether cotton pantiliners are subject to that same leniency. Therefore, while it is not halachically prohibited to use cotton pantiliners when you are tehorah, they may not prevent you from becoming niddah if you find stains on them.
If you do use pantiliners when you are tehorah and would like to use more "eco-friendly" feminine hygeine products that would help you to avoid becoming niddah, we suggest you look into using cotton, reusable pantiliners that are colored. These would prevent staining from rendering you niddah. Some brands include www.lunapads.com, www.gladrags.com, and (in Israel) www.cottna.co.il.
Please feel free to get back to us with any further questions.