Can I use a microcontroller to control the output voltage of a switching powersupply?
You can control an LT1377 with a microcontroller but not directly in the manner that you imply.

Agh - system trashed my answer :-( - I'll blame Olin :-)
 Again and briefer.

LT1377 datasheet here 
See circuit diagram below. 

(1) PWM output voktage fed back to pin FB.
 Place a transistor in series with R2

As PWM duty cycle = switch on time decreases the voltage at FB will decrease and Vout will rise to compensate. PWM output from R1 will need to be filtered and loop response time will increase. 

(2) Add external error amp. Feed R1/R2 output to a comparator. Other terminal of comparator = DC derived from PWM from microcontroller. This has the advantage of working at the speed of the comparator and can be as fast as the IC was originally. This is probably the technically best solution at the cost of one comparator section. 

(3). Feed voltage from R1/R2 AND filtered PWM output into FB pin. As PWM based DC rises it needs less input from R1/R2 to reach Vref and Vout will drop. This is the lowest cost solution. Control range may be imited.