anchan:
You will have to provide a link to the specific encoder you are talking about, however that aside most encoders (incremental and absolute types) are digital in nature and do not provide a variable analog output voltage.
Lefty
<<<<I've been using this encoder, w an analog voltage out:
http://usdigital.com/products/encoders/absolute/rotary/shaft/MA3
Very interesting, I've never never come across an encoder with an analog output voltage before. But back to your question, if you are be powering the encoder with the Arduino's +5vdc voltage source you have no need to provide for or worry about overvoltage protection for the analog input pin in this situation.
Good luck;
Lefty