It's complicated, but also not. Roy's popularity in Smash Bros has little to do with Fire Emblem as a series.
When Melee came out, a lot of younger Nintendo fans had no idea who Marth and Roy were. Melee was their first introduction to the characters. And these characters came with no supplemental trophies or stages. So what people saw of Marth and Roy is exactly what they got.
Marth and Roy were cool because they seemed so "serious" compared to the other Melee fighters. The rest of the cast were cartoon characters, but Marth and Roy seemed much more mysterious and mature.
Nobody knew where they were from (beyond the title of their series), nobody could even understand what they were saying (if they didn't speak Japanese), so what we have are two cool, mysterious characters that felt drastically different from the rest of the cast. Fire Emblem, through exposure, has been largely normalized in Smash Bros. But back then, they stuck out like sore thumbs.
So you have these two cool characters you know nothing about and have no attachment to beyond Melee. You have Marth, who is cool and fast. But then you have Roy, who has a sweet chestplate, red hair, and explodes fire out of his sword. Where Marth was elegant and agile, Roy felt rough and tough. He captured a lot of boyish attitude that appealed to young male players.
Without any other context, Roy was easily one of the coolest characters in the game. There's a reason why he was such a popular "noob" character. He was so new and interesting and had a complex design and EXPLODED INTO FLAMES.
Roy was our boy.
