Hey dude you can still use avrstudio in ubuntu.
Thinking how can you do that .....
Answer is just install wine application and run those windows softwares with wine.
Avr studio, proteus ... even games of windows can be run in ubuntu with wine.
You dont have to even mess with the makefiles blah blah.(just install with wine and get started).
There are many sites to get started with avr MCU's like extremeelectronics , AVR tutorials etc. Just give a google search.
I will tell in detail how to install avrstudio 4 in wine since avrstudio 5 and 6 doesn't work with it but you can use virtual box in linux to run even avr stud 5 and 6 with windows on virtual box.
Open Ubuntu software center and type wine in the search and then install it.
Then get the setup for avrstudio4 and also you need to install win avr
try these links for
a. avr studio 4 http://mycomsats.com/blogs/download-atmel-avr-studio-4-free/
b. win avr http://sourceforge.net/projects/winavr/files/WinAVR/20100110/WinAVR-20100110-install.exe/download?use_mirror=kaz&r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwinavr%2Ffiles%2F&use_mirror=kaz
3.Open the folder where the setup for AS(avr studio 4) is and then right click and then open it with "windows wine program loader" or "a wine application".
4.Then you need to click on the next buttons as you would do it in windows.
5.Then again install win avr similarly with wine(go into the win avr setup ....).
6.Download the classic menu indicator from ubuntu software center. You will get to know about it in just five minutes.
7.From the classic menu -> wine -> Programs -> avr tools
the sixth step is an extra step so that you dont have to mess with where the avrstudio4 executable option is in the wine folder.