Your question touches on the subject of trademark rights vs trademark registration.
Trademark rights are created by use. At common law, these rights extended to the specific goods used in a particular geographic area. At common law, a user may be able to stop another from using a confusing similar mark within that particular geographic area. By registering the mark with the PTO, a trademark holder is able to extend these rights nationwide (subject to prior common law users - but such users are then limited to using the mark to their geographic area).
Also, there are other advantages to federal registration: there is a presumption of trademark ownership and validity in any subsequent litigation involving the trademark; registration also creates what is called "actual notice" or "constructive notice" and therefore informs all parties that the trademark is the exclusive property of the trademark owner; registration also allows for greater remedies in the event of infringement, i.e. recovery of profits or damages for trademark infringement; also, after five years the mark may become "incontestable" and thus precluding three grounds for cancellation, including: (1) mark is not inherently distinctive and lacks secondary meaning; (2) mark is confusingly similar to a mark that someone else used prior to your registration and continues to use; and (3) mark is functional.
Regarding the PTO, it is in charge of determing if a mark should be federally registered. Because they do make decisions regarding whether a mark is registerable by compare one mark to another, i.e. is there a likelihood of confusion, which is the same determination used by the courts to determine infringement, it may appear that they are in the "issuance of rights" business, but that it not the case. They don't have the power to issue injunctions to stop infringers or to order damages in the event of an infringement. They are only concerned with whether a mark should be registered.
I hope this helps.