Uncoupling, Genetic Correlation & Natural Selection
One explanation is that during the transfer of the genes, the genetic code of the child is "uncoupled," rather de-linked, in the process, and goes on to develop in the context in which the genes find themselves. In other words, Professor Simons explains uncoupling like so: "This happens if a trait is influenced by different genes in males and females, if it is under control of genes located on sex chromosomes, or if gene expression has evolved to be dependent on context (whether genes find themselves within a male or a female genome)." The link to this Scientific American article is included below.
Genetic correlation, which is the shared genetic basis of two traits (such as nipples), occurs. It is called an evolutionary "default" when males and females shares the same traits due to genetic correlations. Thus, men acquire the trait of nipples due to this default.
In regard to evolution, there is a process called natural selection. During this process, animals with the most beneficial traits suited to their environment will survive and those traits will be passed on to their offspring. For nipples, it works the same way. As Simons reports, "the presence of nipples in males is probably best explained as a genetic correlation that persists through lack of selection against them, rather than selection for them."
Sometimes natural selection makes sense and sometimes it doesn't. It seems that men have nipples due to an evolutionary default in the natural selection process. So to answer the age-old question, "why do men have nipples," the simple answer is because women do.