Angiokeratomas: These are small, dark red to purple spots that can appear on the penis, among other areas. They are usually benign and can be caused by various factors, including aging, trauma, or certain medical conditions. Their appearance as small red dots and the fact that they are not HSV2 make them a plausible initial consideration.

Folliculitis: An inflammation of the hair follicles, which can cause small red bumps or dots, especially if the penis has hair. This condition can be caused by bacterial or fungal infections and is relatively common.
Pearly Penile Papules: These are small, harmless bumps that appear on the edge of the penis in many men. While they are not typically red, their appearance can sometimes be confused with small red dots, especially if irritated.
Eczema/Dermatitis: Skin conditions that can cause redness, itching, and small bumps or dots on the penis. Allergic reactions or irritant contact dermatitis could present with such symptoms.

Syphilis (Secondary): Although less common, syphilis can cause a rash that might appear as small red dots on the penis. Given the potential severity of syphilis if left untreated, it's crucial to consider this diagnosis, even if the patient has been tested for HSV2.
Basal Cell Carcinoma or Squamous Cell Carcinoma: While rare, these skin cancers can initially present as small, unusual growths or spots. Early detection is key for effective treatment.

Kaposi's Sarcoma: A type of cancer that can cause lesions on the skin, including the penis. It's more common in individuals with weakened immune systems, such as those with HIV/AIDS.
Lichen Planus: A condition that can cause an itchy rash on the skin, including the genital area. It might appear as small, red, flat bumps.
Bowen's Disease (Intraepithelial Neoplasia): A form of skin cancer that can appear as a small, red, scaly patch on the penis. It's considered a rare condition but is important to diagnose early.