Think about it...
If EA releases a Madden game, and it can be completely modded, meaning rosters can be easily updates MID FRANCHISE, schedules can be modded to accurately reflect real life schedules, ratings can be edited mid franchise based on players performance in real life, draft classes can be edited, etc...why would a gamer NEED to keep buying the game every year? Sure, if they made drastic, worthwhile improvements every year, then people would probably keep buying the game. But seeing as how EA is known for not making those huge improvements year to year, a PC gamer could just say "Hey, I can make most of these changes on my own with the mod"
So, while it may have to do with fiscal reasons, the main reason behind that is because modding would almost give Madden something to contend with. Granted, it would be contending with itself, but if EA had another stretch run like 2005-2008 where it was basically just roster updates with some crappy new features, Id much rather just use a mod to update everything than shell out 60 bucks.