The major criticisms of the ideas in this book today are not really different from the major criticisms of those ideas in the past. The major criticism is that Machiavelli's ideas are immoral and unethical. This is why we use the word "Machiavellian" to describe someone who is dishonest and ruthless in his or her quest for power.
The major problem that people today have with the book is that it pays no attention to right or wrong. The book simply talks about how to keep power over the people that one rules. This is very much opposed to our modern ideas in which leaders are supposed to work for the benefit of their people, not simply in order to keep their own power intact.