I think the whole 'Pats are cheap/Kraft is cheap' comes from two sources: opposing fans and never-satisfied Pats fans who are looking for something or anything to support their agenda.
I can recall in 2001 nearly the entire country cheered the Pats on. By the time the Pats were playing for the AFCCG two years later the sentiment had turned; I can recall people already saying 'I'm sick of the Pats winning all the time'. From there people just looked for more reasons to back up their dislike because most are not honest enough to admit it is simply because they want someone else to win. The result was focus on Belichick's attire, second guessing their philosophy for adding Dillon to the team, etc. When the Pats stuck to their philosophy in regards to players and the salary cap, that gave ammunition to opposing fans that the Ptas were cold, heartless, not loyal, and cheap when they let well known veterans sign with another team as free agents.
The other part of the Pats/Kraft being cheap comes about from the simplistic focus on high priced players. If a team does not extend or resign a high priced veteran free agent, there are going to be some that immediately labe the team and ownership cheap. The Pats come more under that microscope because they are more in the public eye due to their success, and also because their business philosophy in regards to the cap probably results in more players being let go. Most that say words to that effect do not take the cap or budgets into consideration, and live in a make believe world where all players should be paid whatever they want, stay as long as they want, and at the same time the team should win a championship every year.
The thing is what is not looked at in those discussions is how the Pats spread the money throughout the entire roster. The thing is, a team not resigning a $5 million/year starter is newsworthy; a team not re-signing two or three $1 or $2 million/year players is not nearly as newsworthy.
We also notice this more because (a) we are pats fans, and (b) the Pats are relevant. For example, does anybody recall any talk about the Bucs being cheap when Warren Sapp and John Lynch finished their careers elsewhere, or when they cut Derrick Brooks? Did anybody blast the Ravens for letting Bart Scott go? The Jets were lauded for picking up LaDainian Tomlinson, but did anybody blast the Chargers for being cheap for letting LdT walk?
Bottom line is that the vast majority of the 'Kraft is cheap' talk comes from people with an agenda: most typically from people looking to get under the skin of Pats fans. Almost all of that commentary is without merit.