Step 1: Understand the sentence.
The phrase
\[
\text{``every day''}
\]
indicates a habitual or regular action.
Step 2: Choose the correct tense.
Habitual actions are expressed using the Simple Present Tense.
For a third-person singular subject (He), the verb takes -s or -es.
Step 3: Analyse the options.
• (A) comes -- Correct. It is the Simple Present form suitable for a habitual action.
• (B) has come -- Incorrect. Present Perfect indicates a completed action.
• (C) had come -- Incorrect. Past Perfect refers to an action completed before another past action.
• (D) coming -- Incorrect. It is a participle and cannot be used alone as the main verb.
Step 4: Final conclusion.
\[
\boxed{\text{He comes late to the class every day.}}
\]
Hence, the correct option is \(\boxed{(A)}\).