There is no official statement as to why Normandy is not used for strikes, but here it is probably related to the fact that strikes by starship guns tend to level the entire area. Quite often, enemies are located in areas that you want to enter or otherwise not to destroy.
That is the first part, related to firepower.
The second is related to the nature of Normandy:
Normandy is a stealth vessel, a submarine in space if you will. It is not a strike craft. While Normandy can hide itself in space, for a limited amount of time, it can be seen from a planet's surface where anti-starship guns can target it. Furthermore, since the ME fields needs to be generated to allow the ship to fly in gravity fields, its shields are weak. In one of the ME books (I forgot which), a frigate was destroyed by a shoulder launched anti-ship missile launcher in the atmosphere.
Often, the Normandy operates in areas that the enemy is heavily entrenched in and as a result, trying to approach these areas for high-precision attacks, is far more risky than just taking the site on foot. For example, on Feros, trying to attack the Geth dropship would have had every Geth gun target Normandy, which is not build for extended combat.
Talking with Anderson and Presley, they will tell you that Normandy is ideal for stealthy insertions rather than combat. In other words, being a "bus". It has teeth, but it should only bare those as a last resort. Its primary method of dealing with enemies is to hide and run, not stand and fight.
This is best seen in the opening of Mass Effect 2: the moment the Normandy is noticed by the Collectors and it fails to hide and run, it suffers catastrophic damage.
