El autobús se atrasa cuando llueve.

The se makes atrasar into atrasarse, turning a transitive verb (“to delay something”) into an intransitive/pronominal one (“to be delayed”). Without se, atrasar needs an object:

• La lluvia atrasó el autobús. (The rain delayed the bus.)
  With se, the subject undergoes the action itself:
• El autobús se atrasa. (The bus is delayed.)

Yes. Retrasarse is a synonym of atrasarse in this context. Both mean “to be delayed” or “to run late.” You’ll hear either version in Latin America:

• El autobús se retrasa cuando llueve.

After cuando (“when”), Spanish uses the indicative if you’re talking about a habitual or factual action:

• Cuando llueve, se atrasa. (When it rains, it’s always delayed.)
  You’d use the subjunctive only for future or uncertain events:
• Cuando llueva, te llamaré. (When it rains [at some future time], I will call you.)

Cuando llueve implies a regular, expected condition (“whenever/when it rains”).
Si llueve means “if it rains” and introduces a condition that may or may not happen. Compare:

• Cuando llueve, el autobús se atrasa. (Habitual: every time it rains.)
• Si llueve mañana, el autobús se atrasará. (Conditional: in case it rains tomorrow.)

Using the definite article el with a singular noun often expresses a general truth or habitual fact about that entire category:

• El perro ladra. (Dogs bark.)
  Similarly, El autobús se atrasa cuando llueve can mean “(Any) bus runs late when it rains” or refer to “the usual bus” on a route. Using un autobús would sound like you’re talking about some unspecified single bus, not a general habit.