When installing a tile floor, its best to use the proper materials for each particular task. Mortar and grout are different products with different uses.
Thinset mortar is an adhesive and binds the tile to the subfloor beneath. Grout is a filler used in the joints or gaps between the tiles. The products aren't interchangeable. Using mortar as grout to fill in the cracks could cause problems for your floor over time.
Mortar as an Adhesive
Made up of a variety of polymers, latex additives, pigments, sand, cement and lime, thinset mortar is the base for tile installations. It's meant to be used as a bonding agent for bricks and heavier stone, rather than lighter ceramic or glass tile. When the cement and lime bond together they create a sticky adhesive that hardens over time and binds the tile to the floor.
Thinset mortar is either gray or white, which doesn't always work well as a grout. There are no pigments added to mortar for matching color like there is with grout. Thus, the mortar can take on a dirty appearance over time and look dingy even with regular cleaning.
Grout as a Filler
Grout is similar to thinset mortar except that it has a higher quantity of sand and less lime. so it's much thinner mixture. Grout is intended to fill the voids between the tiles rather than bond the tile surface to anything, so it's less sticky than traditional mortar. Grout also cures differently because of it takes more water. One of the bigger benefits of grout is that it comes in many different colors so it can fit into any design scheme. Darker grouts also hide dirt so it doesn't look dingy over time.
There are two types of grout. Sanded grout, which is thicker and stronger, is best for larger tiles that have long grout lines to fill. Unsanded grouts are best for areas of 1/8 inch or less.
Using Mortar Instead of Grout
Because mortar is thicker than grout, it's not recommended as a grout substitute for most tile projects. The mortar doesn't flow as grout does, and can leave gaps or holes behind as it dries. Over time, the mortar can crack and weaken or cause water to leak through. Only use mortar in place of grout if the tile specifically calls for it.
Always check the manufacturer's instructions on grout and tile packages to ensure you have the proper product for your particular job.