I understand why Salesforce does not default users to Flow users. However, is there a reason to not check off the Force.com Flow User checkbox when adding a new user?
In general, if a feature license requires you to pay for the license, then the answer comes down to money. Did you buy enough licenses for every user in your org to use that feature.
If the answer is yes then rock on with your bad self. Turn that on for everyone.
If the answer is no then of course, you'll have to be selective.
As to this particular feature license, I think we charged for it initially...a long time ago. But I don't recall if we charge for this anymore in production orgs.
If a feature license is a legacy license and it is now free for everyone, then go back to the yes part above.
Finally...if there are users you just don't want using the flows at all...then why tick the box?