The short and sweet: Mods work just fine, so long as you jump through a few hoops.
The longer answer: Mods right now, especially those with ESP files, are being created with FO4Edit. I would be remiss in not pointing out some history: When Skyrim came out, modders created mods using TES5Edit / TESSnip, and, a few months later, it was found that those mods could break save games. Now, it is my personal opinion that many of the ESP mods created today are safe (including mine, obviously), but if you want to be ultra-super-careful, you should wait for the GECK to come out to use mods.
As for patches "breaking" mods, the only real thing there was that Bethesda closed some "holes" that mod-users were using (such as access to the in-game Data Files menu that was hidden in the launcher). Plus the game will, currently, erase your plugins.txt file if you don't set it to read-only.
Safest mods to use currently are textures. I do use one sorting mod that modifies item names. I consider that one safe.
Rest are waiting for the Creation Kit.