I sugesst, give it a try. It works, you can setup a pallet and its pretty simple to use. On the other hand, there are other tools especially made for pixel art. What you prefer and what you are going to miss can no one else tell you. 

I'm a software engineer, not a graphics person. My opinion is pretty limited with graphics but I've played around with paint.NET out of curiosity.

You can do a lot of good things with Paint.NET and it's a good step to learn how to use more complicated and advanced programs like GIMP and Photoshop. If you want something specifically for pixel art I've tried several things but my skills are very limited. I read this discussion on the RPG Maker forum that might give you some better information:

forums.rpgmakerweb.com/index.php?/topic/5027-software-for-making-pixel-art/

Don't worry so much about your English. The purpose of a conversation is to talk, you don't need to talk perfectly!

I do use Paint.net and it does support transparency.

Was a trouble finding out how it works, but u can use the magic wand ( or whatever its called) and press delete, and it will give you transparency.