It certainly has had a substantial negative effect on open source software.
GPL has been the cause of innumerable compatibility headaches and rewrites and lawyering. All sorts of otherwise useless and counter productive work as well as causing all sorts of headaches for people that want to use it in all sorts of difference scenarios.
What the GPL does though is a allow people to produce and distribute software without some competitor turning around and using copyright law to screw them over.
This is using a lesser evil (GPL) versus greater evil (abuses of the market through copyright law). It is only necessary because of the legal framework the software must exist in. Without the specter of abuse through the use of copyright laws to stifle competition then GPL would be a terrible thing.
Right now it's a very mixed bag. Hopefully the protections it offers against the law offsets the negatives it introduces. I have the view that generally it does.