What programs do I need to use to view and edit Protected Tile Data?
Because I've learned from my experience that there are lots of ROMs out there that are protected against normal programs such as TileMolestor, TileLayerPro, and YY-CHR.
What you are referring to is compressed data, which was mainly done to save space. When tile data is stored uncompressed it is usually when those graphics needed to be loaded to VRAM quickly and there wasn't time to decompress them before the next frame was needed (ex: playable characters). There are ways around that though, such as the case with Super Castlevania 4. The player graphics are compressed, but they are decompressed to WRAM when the game boots up and just uploads from WRAM to VRAM as needed.
To answer your question, there is no single program that can deal with compressed data, mainly because each game handles things differently (most SNES games used a variant of RLE or LZ/LZSS compression). If no one has already created a tool for the game you want to edit, you are going to have to get a debugger emulator (Geiger's or BSNES+ in the case of the SNES) and learn to read and understand ASM. Once you locate the decompression routine and understand what it does, then you can program a tool to decompress the graphics. Decompression is the easy part, the game gives you the blueprint for that, coding a recompressor can be a bit more difficult. It takes a lot of work, but it's doable if you put your mind to it.