TL;DR Silvergate's choice of examples to introduce his book does not address the quoted thesis at all (that average professionals unknowingly commit felonies), and thus one can assume the whole book fails to support his thesis.

I skimmed the sections of his book available on Amazon, and didn't see any proof for his claims. Admittedly, this is only a sampling of the book, but the claims he does make don't justify his position. For example, there is a section which begins Consider some of the cases that will be discussed in more detail further on in this book: I'll address each case he lists in this section, under the assumption that these are some of his strongest arguments.

Text double-quoted below is not quotes from his book, but rather my own short summary of what the charge was and a link to a relevant news article or Wikipedia.

Case #1

A lawyer was convicted of obstruction of justice for destroying a laptop which had child porn on it which belonged to the former music director of his church. He also pled guilty to knowing about and failing to report the music director's abuse of children. (ref)

Silvergate frames this as being indicted for destroying contraband rather than keeping it, and says "therefore holding, rather than destroying it, arguably would be criminal."

This is really a lose-lose situation for the lawyer, because he knowingly took possession of contraband. Either he's convicted for destroying evidence of a crime (and he was a lawyer, so knew it would be relevant), or he's convicted for possessing it in the first place. (Side note: If he had turned it over, it's unlikely he would have been in any trouble for temporarily having someone else's laptop.) But this is not a common situation, and most people will never encounter it.

Case #2

Michael Milken pled guilty to six counts of securities and tax violations. He may have been pressured to plea instead of fighting the charges by a promise from federal prosecutors not to prosecute his brother, who was indicted with him.

Silvergate claims that one of these six was later ruled (in a trial against someone else in the conspiracy) not to constitute a crime. I don't know which one, and without the full book, I can't research this more.

Case #3

Arthur Andersen & Company destroyed documents related to Enron before receiving a subpeona for them, and was convicted of obstruction of justice. The Supreme Court later reversed this.

Silvergate claims this was the "normal document-retention-and-destruction policy" of the company, which may be true. However, to the best of my knowledge no employees of AA&C were charged for the actions - just the company itself.

Thus, this is one that can't be part of the "three felonies a day".

Case #4

Steve Kurtz was arrested for mail fraud for mailing non-infectious bacteria as part of art exhibit. In 2008, the charge was ruled "insufficient on its face", meaning that the actions were not a crime in the first place.

Silvergate claims this charge was simply a way to justify the time spent investigating Kurtz for bioterrorism due to his art.

This one is irrelevant to Silvergate's argument. Kurtz was convicted for something that wasn't a crime, and thus can't be an example of a felony.

Case #5

I'm not even going to research this one: The DoJ "reportedly looked into" indicting the New York Times for espionage for their reporting of the NSA's warrantless surveillance programs. Since it was just "looked into", there's nothing relevant here. Since it was (again) a company, there's doubly nothing.

This section concludes (actual quote from Silvergate):

These are just a few of the prosecutions in which well-meaning professionals from all walks of life have been charged (or nearly charged) criminally for engaging in activities that most of us - lawyers and laymen alike - would consider lawful, often quite ordinary, and frequently socially beneficial.