I think those who argue for patents have to show how exactly patents promote entrepreneurship and innovation.
What patents do is to boost the value of ideas relative to execution. They are supposed to help individuals with great ideas but without access to the resources required to execute on them.
For patents to make sense, there has to be a very large gap between the capital required to work on the idea itself and the capital required to bring it to market. Something like building a factory or conducting 10 years worth of clinical studies. Something that enables a big encumbant to copy an idea and win every time against the original innovator.
I don't think that is generally the case in the software space. It is certainly more true for enterprise stuff that you need sales people for and that's why MBA types may think more favorably about software patents. But even for that kind of software, the gap isn't nearly as large as for inventing a new type of nuclear reactor or jet engine or cancer drug.
Another problem with patents is that they are supposed to make people publish their research instead of keeping it secret, but many small companies and individuals cannot afford to go through the patenting process.
I can say for myself that I do not publish my research nor do I open source it. Secrecy is the cheapest option to have a head start with exactly the kind of ideas that might really benefit from patents. Ideas that you don't think someone else could have tomorrow by accident or by gradually expanding on existing ideas.