No Stupid Questions

As others have already said, you go with the initial sound rather than the written letters. The written word is mostly built around conveying speech, so the rules fit what you would use if reading out loud. There are plenty of cases where writing conveys other cues than verbal, but the core of it still applies to sound.

That actually applies to most punctuation as well, depending on how one defines "most".

Any initialism is going to be counted as the first letter being a word for the purpose of a/an usage, when said letters are pronounced as letters. In the case of RTS (an initialism), you wouldn't ever say it as a word, unlike RAM, which is almost always pronounced as a word and is thus is an acronym. That's the difference between those things, btw. We tend to call all of them acronyms, and that's okay, but there is a difference.