I have not had any problems so far.In fact its a welcome change for my mouse to get constant use of hte other button!! What i do like is that to fire u just keep it pressed and dont have to keep clicking! Using it as is the only changes i made was i put my mousewheel button as afterburners and the tab key i mapped to cruise mode cos in certain situations i made a mess of trying to do hte standard key to go to cruise trying ot out run some people , tab just seems easier to toggle cruise mode on and off, for me anyway.
The only pet peeve i have is there is no apparent way to map anyhting ot the sub menus of filtering the main display for loot,ships or whatever. I'd like ot be able to do that while flying and not come out of free flight to use the mouse to click on them, but thats just a small issue.
Also having a 5 button mouse really helps with mouse4 and 5 doing missiles and mines i just let my thumb do the countermeasures on the 'c' key

I have to admit that having fps-like controls in a space sim is pretty cool. However, I agree that some of the mappings are funky.
I expect DA will get enough complaints that they'll allow remapping of all functions save f1 by the first patch.
They've already done the hard work creating a pretty slick game. It seems that taking the effort to add this flexibility is a no-brainer.