You have to apply any mods again once you update. All of minecraft's important files are stored in one big file (minecraft.jar). That file is deleted and replaced with the updated version when updating, so any mod you applied to it will also be lost.
I would recommend using MultiMC (http://www.minecraftforum.net/topic/1000645-multimc-43-windows-linux-mac/). Basically it stores copies of the older versions, and all the mods needed to run each instance you make. You can save many configurations, and do not have to modify the "minecraft.jar" directly. This way you can never accidently update over it or anything, or ruin a mod build permanently. It takes a little getting use to using, but once you do you'll wonder how you ever modded Minecraft without it!