I have to say that those who play the upright bass are not always male, but I would think that instrument as well as a tuba, might tend to be used more by men because of the physical strength required to move and hold such an instrument. That does not mean it is impossible: I have a good friend who plays the upright base, but it's not something I notice many women carrying. Of course, apparatus available now to move certain heavier/larger instruments may make this concern a thing of the past.

Part of the reason for gendered instrument preference relates to tonal qualities of the instrument. In general (of course there will be exceptions), females have preference for more higher tonal frequencies than males, while males have preference for more lower tonal frequencies than females. A tuba and the timpani may require larger body size and strength but also require preference for (or even tolerance for) lower tonal frequencies, while oboes and piccolos may require lesser body size and strength but also require preference for (or even tolerance for) higher tonal frequencies. 

Stereotyping probably part of the reason some instruments seem to be played more by one gender than another.  It may also have something to do with other factors such as the size of the instrument.  The tuba, for instance, is generally a large instrument.  Many students begin learning to play a particular instrument at a young age.  Since females tend to be smaller and less muscular than males, it is no surprise that a young lady would not choose such a large and bulky instrument.  Something similar might be said for the flute.  Usually, little boys are a rougher and little girls more willing to be gentle.  The flute is a delicate instrument.  Little boys might not be encouraged to play the flute because they tend to be rough and it is a fragile instrument compared to others.  Of course, even these reasons are based on stereotypes.

A lot of the difference is stereotypical and historical. Many years back, certain instruments were considered to be masculine, and others feminine. In general, instruments that required a lot of physicality to play (such as percussion and trombones) and larger instruments were mainly played by men. Instruments that were physically smaller or that produced a more delicate sound (flutes, oboes) were played by women. Women cellists were rare because the spread-knee posture required to play the cello was considered to be terribly unfeminine and improper.

Another factor is simply size. Most people begin music lessons when they are still quite young, and there is a tendency to match the instrument to the child's physical size and capability. While it reinforces the stereotype, there is no point in giving a child an instrument that is too unwieldy for them to handle - they will most likely give up. Many of the people who play outside the stereotypes seem to have switched instruments at some point after they learned to play. In college I played tuba in the orchestra, and I'm a 5'5" female. However I was able to both store and practice the instrument in the music building. If I had had to carry it around campus a lot that would have been a different matter. I also would never have been able to play tuba in high school band, because I had a long walk to the school bus stop, and rode a crowded bus, so I would never had been able to take my horn home to practice. In high school I played the trumpet instead, which was much more manageable physically.

While there are certainly plenty of examples to the contrary, the guitar, at least in the popular imagination, is usually associated with men. When we think of rock guitar players, for example, they are predominately men, as is, frankly, the field of rock music in general. It seems to me that the trend is moving in the opposite direction, though, especially in indie rock and non-mainstream music.

Stereotyping can even be found in music. When I was in junior high band (in the 1960s), there were no male flute players and no female tuba players. Trombones were dominated by males, clarinets by females. Times have changed a bit, but some heavy instruments--such as the tuba and marching bass drum--are still mostly played by males. Others that require strong lung capacity, such as the bass sax, are usually played by males as well. But with equal rights for women also came a change in the perception of what instruments women can play, and for the most part, instruments are played without regard to gender today.

I think stereotyping is a huge part of the situation. There are some physical practicalities - tubas or sousaphones are large and heavy and would be phisically difficult for many females to manage in a marching band. However, James Galway plays the flute and penny whistle with a sound that is heavenly to hear; the current first seat percussionist in my town's high school band and orchestra is female; there are examples to refute the assumption for every instrument.

I have no data to support my ideas, but I have watched students play in bands for many years. While many instruments do seem to be genderless, some of them are clearly more typical for one gender than the other. Some of it is probably physical; for example, a flute-player should not have huge fingers and a tuba player has to be able to hold the tuba. Some of it is also probably based on stereotypes. What I found when I taught in smaller schools, though, is that students had to "fill in the gaps" of the band and played whatever instruments were needed when they joined the band, regardless of the stereotypes--and no one in the audience was too surprised at who was playing what.

Two instruments come to my mind immediately... the drums and the flute.  While I have known a few female drummers, it is an instrument dominated by males.  Likewise, there are some male flautists, but it is an instrument that is predominantly mastered by women.

With the tuba, I suppose it might be a lung capacity thing.  As far as other things, I would guess that has mostly to do with what people are used to.  You see lots of women playing harp and you don't think (as a man) that that's an instrument for you.