If you understand symbolism the way contemporary man does, then that should upset you. In response, you might consider looking to a more ancient theological understanding of symbolism. A symbol, then, is not a mere sign pointing to what it signifies; rather, it reveals what it signifies in such a way that it actually contains it without limiting the thing signified to the revelation in the symbol.
That is to say: A stop sign is not a symbol, nor are those arrows that label this button the one that fast forwards. Consider instead the human body. Human beings are ensouled bodies; our souls cannot communicate with each other without the use of our bodies (whether that's to act or even just to speak or write). In this way, our bodies symbolize our souls, without reducing our souls to only that which is communicable via the body.
This view of symbolism is parallel to one of iconography, wherein Jesus Christ is the icon of the Father, because He communicates Him to humanity in a way we can understand. (He is, after all, the image of the invisible God.) In this vein, theological tradition calls Him the primordial sacrament.
The Church, then, is called the fundamental sacrament, for as Christ made present to us on earth the Father in heaven, so does His Church make Him present to those of us who have not seen Him in His glorious humanity, yet still believe.
A sacrament, even in this broad sense, is a particularly efficacious symbol that communicates the grace it signifies; the grace presented in the sacrament is actually present within the sacramental symbols. It is through this lens that we look at Holy Mother Church.
Yes, the Church is an institution, a group of fallible human beings who screw things up. But she is also the Bride of Christ, guided always by the Holy Spirit. Just as Jesus Christ is God and man, and as every human being is body and soul, so is Holy Church divinely guided, though she is led by mere humans.
And there is my point: "she is led". By referring to the Church as she, one immediately evokes her many images: Holy Mother Church, the Bride of Christ, Our Lady, even the moon (who shines brightly with a light not her own). By referring to the Church as she, one linguistically gives credence and support to the Bride of Christ, who is docile to the guidance of the Holy Spirit.
In such a day and age as ours, when Holy Mother Church is seen as just another corrupt institution with too much bureaucracy and too little relevance, referring to her with love is one of the best (and simplest) ways a faithful Catholic can work to restores faith in her as a reflection of Christ, thus containing His authority and power (among so many other things).
One of the most remarkable things about Holy Mother Church is that this personification of her is not inaccurate. One can enjoy her beauty, delight in her treasures, and trust in her guidance. Some lucky few (a blessed few, really) even have the privilege of marrying her.
This may all sound romantic, but it's simply realistic. Before Our Lord gave up His spirit on the cross, he entrusted St John to his dear mother; likewise, He has entrusted each of us to His Church. Let us always love her with His love, and may we in return receive from her His great blessings. If you place your trust in Holy Mother Church, you will never be far from our dearest Lord.
Accept and bless these gifts [. . .] which we offer you first of all for your holy catholic Church. Be pleased to grant her peace, to guard, unite and govern her throughout the whole world...
-Roman Canon, newly approved translation (p16)