Are rogues in 3.5 marginalized by magic? In other words do spells infringe on the rogues role in the party?
A better phrasing may be that magic infringes on all skill users.
No. Rogues are as marginalized as the player allows himself to be.
Because the rogue's player can always leave the campaign?No. Rogues are as marginalized as the player allows himself to be.
Magic can do anything a rogue can do but better so yes, it does marginalize the role of the rogue.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.